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According to Wikipedia:

The Gospel [of John]'s authorship is anonymous. Its Chapter 21 states it derives from the testimony of the 'disciple whom Jesus loved.' Along with Peter, the unnamed disciple is especially close to Jesus, and early-church tradition identified him as John the Apostle, one of Jesus' Twelve Apostles. The gospel is closely related in style and content to the three surviving Epistles of John such that commentators treat the four books together, yet, according to most modern scholars, John was not the author of any of these books.

Assuming the author can be identified with disciple whom Jesus loved, Wikipedia gives us a number of possibilities:

  1. John Zebedee
  2. Lazarus of Bethany
  3. Mary Magdalene
  4. Judah, son of Jesus
  5. Unknown priest or disciple
  6. Both Lazarus and Martha's son
  7. Jesus' bother James

This seems a comprehensive list (especially with the inclusion of #5). Can we pare it down by eliminating any clearly speculative suggestions? Can we re-order the list according to which are most likely?

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Are you asking for the identity of the beloved disciple, or of the author of the gospel? They may not have been the same person. –  Bruce Alderman Feb 7 '12 at 20:50
    
@Bruce: Good point. I'm really interested in getting the main arguments for who wrote John, so I amended the question. Perhaps I should divide it into two separate questions, however. We have a good answer on "Who was the Beloved Disciple?", so maybe I should ask the authorship question as a second post. –  Jon Ericson Feb 7 '12 at 21:04
    
@Bruce: On second thought, I asked another question to cover the authorship angle. –  Jon Ericson Feb 7 '12 at 21:39
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3 Answers

up vote 8 down vote accepted

The gospel of John only gives a few clues to the identity of the beloved disciple.

  • John 13:23 indicates that this disciple was seated next to Jesus at the Last Supper.
  • John 19:27 indicates that he took care of Jesus' mother after the crucifixion.
  • John 20:2 indicates that he went with Peter to see the empty tomb.
  • John 21:7 indicates that he was present when Jesus appeared to Peter and asked him the threefold "Do you love me?"
  • John 21:21 refers to a rumor that this disciple would never die.
  • John 21:24 indicates that his testimony is the source for this gospel.

Leading Candidates

  • John, son of Zebedee: This is the traditional answer. The second century bishop Irenaeus of Lyons—a disciple of Polycarp, who in turn was a disciple of John—says John was "the disciple of the Lord, who also had leaned upon His breast," a reference to John 13:23.

    Aside from tradition, this view is supported by comparison with the synoptic gospels, in which John is one of Jesus' inner circle.

    John was also one of the 12, who according to Mark 14:16-17 shared the last supper with Jesus.

    Finally, John was a fisherman before being called by Jesus, according to Matthew 4:21.

  • Lazarus: Ben Witherington has suggested this name based on the statement in John 11:5 that Jesus loved Lazarus and his sisters. Before this point, the gospel does not mention a "disciple whom Jesus loved".

    Witherington also suggests that Lazarus was the "other disciple" of John 18:15, who was known to the high priest and was able to get Peter into the courtyard. Lazarus, as a native of Judea, would be far more likely to have this access than John the Galilean fisherman.

    Finally, the sons of Zebedee are named in John 21:2, while the beloved disciple is mentioned later in the chapter.

  • James, brother of Jesus: This is based on Jesus' statement to Mary, "Here is your son" in John 19:26.

    James also became the head of the church after Pentecost, which indicates his importance and perhaps his closeness to Jesus.

Speculative Candidates

All the other candidates are highly speculative and do not fit the above criteria.

  • Mary Magdalene: the beloved disciple is consistently identified as a man.
  • Both Lazarus and Martha's son: is based on the beloved disciple of John 21 being a different person from the one in John 13-20.
  • Judah, son of Jesus: is not known to have existed.
  • Unknown priest or disciple: if he was that close to Jesus, it is highly unlikely he would not be mentioned elsewhere.

Conclusion

Of these candidates, John is by far the most likely. He is the only candidate that fits all the criteria. He has also been identified as the beloved disciple since the early days of the church.

Lazarus is an intriguing possibility, but since he is not even mentioned in the other gospels, it's hard to see how he could be considered closer to Jesus than the 12.

James makes sense based on familial connections, but the gospels do not indicate that he was a disciple of Jesus before the resurrection.

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A similar question was raised in another Biblical Hermeneutics posting and part of the response posted relates to this question, so I will share it here.

There are facts recorded about John that are mutually exclusive with facts that the author of the fourth gospel tells us about himself. Of course, there is no problem with scripture. Rather this problem only occurs when one tries to force the unbiblical John tradition on the text, in spite of the biblical evidence to the contrary. So the false tradition that has taught people to ignore the biblical evidence and follow after non-Bible sources who claim this unnamed author was John is the cause of the problem.

TheDiscipleWhomJesusLoved.com has a free eBook that presents the biblical evidence that can prove the beloved disciple was not John (including the mutually exclusive facts noted above) and those who care to weigh the biblical evidence on this topic may find this resource helpful as they seek the guidance of scripture when it comes to answering questions about the anonymous author of the fourth gospel.

While a comment claims John "is the only candidate that fits all the criteria" and suggests the John idea "is supported by comparison with the synoptic gospels", the Bible proves otherwise. The truth in fact is the writers of the first three gospels treat John and the unnamed "other disciple, whom Jesus loved" like different people (because they were different people). They freely mention John but never mention the beloved disciple and even omit him when he is playing a material role in the event being described.

The idea that the fourth gospel is 'John's eyewitness testimony' ignores the fact, for example, that it is the only gospel that does not mention the raising of the daughter of Jairus, the Mt. of Transfiguration, and the prayers of Jesus at Gethsemane - though John was one of only three eyewitnesses to these events. In fact, the least helpful of the four gospels, when it comes to learning about the things John witnessed, said, and did during the ministry of Jesus is the gospel which men mistakenly attributed to John.

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It should be pointed out, though, that the first ones to attribute this gospel to John were people who knew him personally, and that the church community that put the New Testament together included this gospel only because it carried John's name and authority. –  Bruce Alderman Feb 9 '12 at 18:06
    
+1 for the last paragraph which is thought-provoking. I would like to encourage you to take a less personal tone when referring to other answers, and while linking to and/or promoting external resources is absolutely fine, it is much more helpful to folk here if you include a brief summary of the content in your answer. Are you willing to do a bit of editing to your answer? There is no need to answer again - editing is generally preferred on the SE network. –  Jack Douglas Feb 13 '12 at 7:40
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I actually could vote this up if you would just mention Lazarus by name in your answer rather than making me download and read a 56-page .pdf to find out who you are talking about. –  Bruce Alderman Feb 15 '12 at 5:34
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We can eliminate #4 as that is based on the speculation that Jesus had a son. Even if he had been married (also speculation), then we would have to assume he married at the normal age for a Jewish male, around 15-18. As he was most likely 33, the child would be 16 at the most (giving the couple a little time to themselves before having a child).

We can also eliminate #7 as the Disciple whom Jesus Loved was one of the Twelve Apostles (present at the Last Supper sitting at the head table and next to Jesus) and James was not a believer until after the resurrection. Also, the article states that this theory is based on a literal interpretation of "woman, behold your son." If the Disciple were James, there would be no reason to state this obvious fact. Such a statement in the NT times was to assign responsibility of a dependent to another person. If this were James, Jesus would not have to say anything as James would accept the responsibility as part of his Jewish heritage to honor his father and mother.

All references to the Disciple use masculine pronouns, eliminating Mary.

We can eliminate most of the others for the reason of the Disciple having to be one of the 12.

At all times we see the Disciple whom Jesus Loved, he is shown to be one of the 12. In John's Gospel, John son of Zebedee himself is never named even though he plays a prominent role in the other gospels. That is the main reason I identify the Disciple with John son of Zebedee.

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I agree with most of your logic, but I wonder if we can be sure that only the Twelve (and Jesus) were at the Last Supper? I agree we can eliminate James (who would not have been there), but I don't know if we can eliminate Lazarus or other disciples who are not among the 12 on that basis. –  Jon Ericson Feb 7 '12 at 19:00
    
Also (and this is a nitpick), I'm not sure couples took "a little time to themselves" in those days. But #4 sure seems like a non-serious contender even without that tidbit. –  Jon Ericson Feb 7 '12 at 19:13
    
According to the rabbinic writings, one of the times "the absorbant" was allowed was after marriage to allow the couple to adjust to married life. The absorbant was a cotton diaphragm contraceptive. I'll add an edit regarding the reason to be one of the 12. –  Frank Luke Feb 7 '12 at 20:20
    
My wife and I had a similar idea about preventing pregnancy for the first year. Our contraceptive failed, however. I've never heard that the concept has any history before the Modern era. Interesting. –  Jon Ericson Feb 7 '12 at 21:09
    
I hope you don't mind, but I shifted the thrust of the question slightly. I think your answer actually fits the modified question better than the original. –  Jon Ericson Feb 7 '12 at 21:38
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