31 “For this reason a man will leave his father and mother and be united to his wife, and the two will become one flesh.”
32 This is a profound mystery—but I am talking about Christ and the church.
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The mystery is Christ and our mystical union to him. Hodge pretty much answers the question as simply as possible:
Τὸ μυστήριον τοῦτο μεγα ἐστίν, this mystery is great. The word mystery does not refer to the passage in Gen. 2:24, as though the apostle intended to say that that passage had a mystical sense which he had just unfolded by applying it to the relation between Christ and his church. It is the union between Christ and his people, the fact that they are one flesh, he declares to be a great mystery. (Charles Hodge, Ephesians p350)
He himself is a great and unfathomable mystery:
Beyond all question, the mystery from which true godliness springs is great: He appeared in the flesh, was vindicated by the Spirit, was seen by angels, was preached among the nations, was believed on in the world, was taken up in glory. (ESV, 1 Timothy 3:16)
To add to this mystery of Christ that somehow every believer is united into a single body in his flesh, is indeed a very great mystery that no man can either fully know or explain. That believers are literally in some mystical sense united to the person of Christ and thus died and risen in him to new life is central to Pauline theology (Col 2:6-15, Eph 3).
This 'mystery' or Christ, or the gospel, as Paul elsewhere refers to from various angles is to be taken as 'a long held divine secret only' now at last disclosed. Therefore even though this mystery is not referring to marriage directly yet that primary institution of human society is now seen as formerly declared in shadowy words at the beginning compared to our understanding in the gospel now. Under Pauline usage, nothing can be understood until the 'mystery of Christ' is put in the centre of our view. It is from this 'great mystery' and our mystical union to him, that Paul resolves all wisdom, meaning and explanation of all truth.
- ΤΟΜΥΣΤΗΡΙΟΝΤΟΥΤΟΜΕΓΑΕΣΤΙΝ (P46, ca. 175-225 CE, et al.)
- "But I am speaking," says [Paul], "of Christ and the Church." (Tertullian, Against Marcion, V-847, ca. 175-222 CE)
- Paul has referred to the conjunctions within the Pleroma ... when writing of the conjugal union ... thus: "This is a great mystery, but I speak concerning Christ and the Church."(Irenaeus, Against Heresies, I-117, ca. 175-225 CE)
- το μυστηριον τουτο μεγα εστιν (TR & GMT)
Eph. 5:32 reads as if Paul might be revealing one of the secretive Masonic mysteries. But, he simply compared marriage to the union of Christ and the church. He makes that plain by the next words: εγω δε λεγω εις χριστον και εις την εκκλησιαν:
"Not calling your attention to the mere human relationship, but to the mysterious relation between Christ and His Church,..." (Vincent, Word Studies).
Looking only at verse 32, it is pretty clear that the profound mystery involves Christ and his relationship with the church. However, looking at the broader passage (probably around 5:21-33) demonstrates that Paul is talking about more. This portion of Ephesians is one of the key passages on marriage relationships, and it is here that Paul explains the marriage relationship as a symbol of the relationship Christ has with his church (compare Revelation 21:9
One of the seven angels who had the seven bowls full of the seven last plagues came and said to me, “Come, I will show you the bride, the wife of the Lamb.”, among other passages).
To summarize the passage, Paul instructs wives to submit to their husbands as to the Lord (as all Christians submit to the Lord). He then instructs husbands to love their wives as Christ loved the church, by giving his life for her. And this is where we find 5:32.
...28 In this same way, husbands ought to love their wives as their own bodies. He who loves his wife loves himself. 29 After all, no one ever hated their own body, but they feed and care for their body, just as Christ does the church— 30 for we are members of his body. 31 “For this reason a man will leave his father and mother and be united to his wife, and the two will become one flesh.” 32 This is a profound mystery—but I am talking about Christ and the church.
It is a profound mystery that a man and woman can be members of each other's bodies. It is a profound mystery that two individuals can become one flesh. In mathematical terms it is like saying 1+1=1, which challenges everything we know and understand. Furthermore, there seems to be a supernatural bond between spouses; this passage tells why. The profound mystery of becoming one flesh and giving up our individual freedom and being supernaturally bound with our spouse highlights the profound mystery of becoming one with Christ and being supernaturally bound to him.
A quick note on the term mystery as used by Paul: it is something that was hidden but is now revealed in Christ.
1 Corinthians 15:45
The first man Adam became a living being, the last Adam became a life giving spirit
If there was a first Adam, then there is a last. If there was a first Eve, then there must be a last Eve. The last Adam is Christ and the last Eve is the church.
God created the church out of the body of Christ. He put Christ into a deep sleep lasting for 3 days. Christ came out of the grave with a hole in his side, the fifth rib to be precise. So in light of this, the mystery of marriage is but a foreshadowing of God's purpose in Christ. (John 19:34, 20:27)
In Gen 2:23, the first Adam said "Now at last, this is bone of my bone and flesh of my flesh"
In Ephesians 5:30, of the Last Adam it is said: "We are members of his body, of his flesh and of his bones.
So this is the profound mystery that Paul was talking about.
Marriage itself was created to foreshadow Christ and his church in the new covenant (Ketubah as the Rebecca park totillo calls it due to the way the covenant was enacted with the apostles)
The great "mystery," "secret" or "sacrament" (μυστηριον) is matrimony itself. Hence he says, "but I speak [here] of the Church" (using the in this context adversative conjunction δε) to make clear he speaks of the matrimonial union of Christ and His Bride, not of marriage in general. Hence, he follows up with, "nevertheless, let each one of you also" (i.e. that isn't Christ, and his bride, who is not the Church).
I'm of the opinion that the common understanding of "one flesh" is incomplete at best. The "one flesh" is not the marriage, or certainly not the entire marriage, but rather the offspring is. That is, when Adam and Eve knew each other "in the Biblical sense" the insertion of his "bone" into her "flesh" was not what made them one flesh but rather the deposit of his seed. It was the child that they produced that was the amalgamation of their flesh.
While not spelled out, that is also what is implied here:
BSB 1 Cor 6: 15Do you not know that your bodies are members of Christ? Shall I then take the members of Christ and unite them ["adhere"] with a prostitute? Never! 16Or don’t you know that he who unites himself with a prostitute is one with her in body? For it is said, “The two will become one flesh.” 17But he who unites himself with the Lord is one with Him in spirit…
Notice that the union of the Christ with the assembly is a "spiritual" one, not a fleshly one. This is the marriage part. The marriage does not make the husband and wife to be one flesh but rather to be one in "spirit". And those joined to the Anointed in spirit become part of his "body", which is a united collection in spirit but not in flesh.
So by "adhering" they "will become" (Ἔσονται future indicative middle of "to be") "one flesh". This of course is citing Genesis 2:24. The traditional interpretation lacks any physical evidence that coitus has any such effect of one flesh but procreation is acknowledged everywhere by evidence and observation that the baby is an amalgam.
Notice that in reference to the wife/assembly, he speaks of one "body" and only at the end he speaks of becoming one flesh:
NIV Eph 5: 25Husbands, love your wives, just as Christ loved the church and gave himself up for her 26to make her holy, cleansing her by the washing with water through the word, 27and to present her to himself as a radiant church, without stain or wrinkle or any other blemish, but holy and blameless. 28In this same way, husbands ought to love their wives as their own bodies. He who loves his wife loves himself. 29After all, no one ever hated their own body, but they feed and care for their body, just as Christ does the church— 30for we are members of his body. 31“For this reason a man will leave his father and mother and be united to his wife, and the two will become one flesh.” 32This is a profound mystery—but I am talking about Christ and the church. 33However, each one of you also must love his wife as he loves himself, and the wife must respect her husband.
So in relation to the assembly there is a spiritual union where they become members of one another but in terms of the offspring, that is one flesh.
So what is the great mystery? The great mystery is, as I see it, what is the one flesh that the adhered, spiritually unified Christ and his body give birth to?
The great mystery is that the Father will have a grand baby or grand babies that is/are the amalgam of the flesh of his son Jesus and the flesh of his son's bride, the assembly aka the new Jerusalem:
NIV Rev 21: 2I saw the Holy City, the new Jerusalem, coming down out of heaven from God, prepared as a bride beautifully dressed for her husband. ... 9One of the seven angels who had the seven bowls full of the seven last plagues came and said to me, “Come, I will show you the bride, the wife of the Lamb.” 10And he carried me away in the Spirit to a mountain great and high, and showed me the Holy City, Jerusalem, coming down out of heaven from God.
YLT Isaiah 62: 1For Zion’s sake I am not silent, And for Jerusalem’s sake I do not rest, Till her righteousness go out as brightness, And her salvation, as a torch that burneth. 2And nations have seen thy righteousness, And all kings thine honour, And He is giving to thee a new name, That the mouth of Jehovah doth define. 3And thou hast been a crown of beauty in the hand of Jehovah, And a diadem of royalty in the hand of thy God, 4It is not said of thee any more, ‘Forsaken!’ And of thy land it is not said any more, ‘Desolate,’ For to thee is cried, ‘My delight [is] in her,’ And to thy land, ‘Married,’ For Jehovah hath delighted in thee, And thy land is married. 5For a young man doth marry a virgin, Thy Builders do marry thee, With the joy of a bridegroom over a bride, Rejoice over thee doth thy God.
Paul says that Sarah, Abraham's wife is the type of the "Jerusalem above", the bride of the Christ:
BSB Galatians 4: 25Now Hagar stands for Mount Sinai in Arabia and corresponds to the present-day Jerusalem, because she is in slavery with her children. 26But the Jerusalem above is free, and she is our mother. 27For it is written: “Rejoice, O barren woman, who bears no children; break forth and cry aloud, you who have never travailed; because more are the children of the desolate woman, than of her who has a husband.”
So Paul says that the bride of Christ is the Jerusalem above and "her" children are all of the faithful:
NIV Psalm 87: 1He has founded his city on the holy mountain. 2The Lord loves the gates of Zion more than all the other dwellings of Jacob. 3Glorious things are said of you, city of God: 4“I will record Rahab and Babylon among those who acknowledge me— Philistia too, and Tyre, along with Cush — and will say, ‘This one was born in Zion.’ ” 5Indeed, of Zion it will be said, “This one and that one were born in her, and the Most High himself will establish her.” 6The Lord will write in the register of the peoples: “This one was born in Zion.” 7As they make music they will sing, “All my fountains are in you.”
I'm still ruminating on this but this is what I believe is the theme of the great mystery.
Thus he composed a more spiritual Gospel for the use of those who were being perfected. Nevertheless, he yet did not divulge the things not to be uttered, nor did he write down the hierophantic teaching of the Lord, but to the stories already written he added yet others and, moreover, brought in certain sayings of which he knew the interpretation would, as a mystagogue, lead the hearers into the innermost sanctuary of that truth hidden by seven veils.
-- Clement of Alexandria
One might find in the Letter of Clement of Alexandria on Secret Mark further explication of points of contention surrounding the question of expansion of the notion of "one flesh" as extended to the entirety of the Church.
I realize this isn't precisely an answer, but the true answer appears to be ineffable (incommunicable by words) by divine design!
Could it be suggested that Paul was also referring to the point of creation when by the Word, Who is Christ (1 John 1:1-14) made the 1st man, Adam, through this mysterious union of Spirit and Flesh and hencforth designed him with the same sort of mysterious capability that involves the act of bringing forth a living being with the ability to house God's Spirit. And then to continue such a divine act in perpetuity is the zenith of God's decree of our undeserving union with Himself.