The death of John the Baptist is mentioned in Josephus, Antiquities of the Jews as well as in both Matthew 14:1-12, Mark 6:17-29, and Luke 9:7-9. Earlier in his gospel, Matthew reported John was in prison in 11:2 but does not narrate the death of John the Baptist after Jesus has been rejected at Nazareth.
Matthew used Mark 6:1-6a for his rejection story in 13:53-58, now he abbreviates Mark 6:17-29. But Matthew separated the mission of the Twelve (Mark 6:6b-13; 30-31) from Mark 6. Matthew does not narrate the mission; Jesus gives authority to the appointed Twelve and sends them out (Matthew 10:1-4) followed by a long set of instructions (the second discourse, Matthew 10). The death of John the Baptist is now orphaned, so Matthew attaches it more closely to the feeding of the 5000 story. “When Jesus heard this” he withdrew privately to a solitary place (Matt 14:13). In Mark 6:32 Jesus simply withdraws with his disciples without explanation.
Does Luke have another source? Luke reports John’s arrest in 3:29-20 as a response to John “reproving” Herod “concerning his brother’s wife” and “all the evil this Herod had done.” Later in Luke 9:7-9, Herod heard about “all that was happening” and the rumor that John the Baptist had been raised from the dead or that Elijah had appeared, or that one of the “prophets of old had risen.”
The report of the death of John the Baptist in Josephus appears in the context of a border dispute between Herod Antipas and the Nabatean king Aretas. Some Jews consider this defeat to be punishment for executing John.
Antiquities 18.5.2 (116) Now, some of the Jews thought that the destruction of Herod’s army came from God, and that very justly, as a punishment of what he did against John, that was called the Baptist; (117) for Herod slew him, who was a good man, and commanded the Jews to exercise virtue, both as to righteousness towards one another, and piety towards God, and so to come to baptism; for that the washing [with water] would be acceptable to him, if they made use of it, not in order to the putting away [or the remission] of some sins [only], but for the purification of the body; supposing still that the soul was thoroughly purified beforehand by righteousness. (118) Now, when [many] others came in crowds about him, for they were greatly moved [or pleased] by hearing his words, Herod, who feared lest the great influence John had over the people might put it into his power and inclination to raise a rebellion (for they seemed ready to do anything he should advise), thought it best, by putting him to death, to prevent any mischief he might cause, and not bring himself into difficulties, by sparing a man who might make him repent of it when it should be too late. (119) Accordingly he was sent a prisoner, out of Herod’s suspicious temper, to Macherus, the castle I before mentioned, and was there put to death. Now the Jews had an opinion that the destruction of this army was sent as a punishment upon Herod, and a mark of God’s displeasure against him. William Whiston, The Works of Josephus: Complete and Unabridged (Peabody: Hendrickson, 1987), 484.
Louis Feldman considers this passage authentic, especially since it differs from the canonical gospels on the reason Antipas executed John. In Josephus, Herod Antipas was alarmed at John’s growing reputation among the people and thought he should “strike first and be rid of him” (Feldman’s translation). Josephus mentions several messianic prophets who gathered a following but were eventually dispersed by the Romans. John is not a messianic prophet such as Theudas (Antiq. 20.5.1) or other “imposters” (Antiq. 20.8.6).
Although Josephus confirms Antipas killed John at Macherus, he does not mention John’s condemnation of his marriage to is sister-in-law or the famous dance which resulted in John’s beheading.