Against Apion is Josephus's last surviving work, written in the late 90s. It defends the Jewish religion against the ridiculous attacks of the Alexandrian grammarian and sophist Apion and other anti-Jewish writers. It also includes the first impressive synopsis of the Law of Moses for non-Jews. He died in Rome around 100 CE.

As an historian, Josephus is thought to be generally trustworthy except when he deals with matters in which he himself was involved. Also, like many classical historians, he often places apocryphal speeches on the lips of personalities and gives Greek colouring to Jewish schools of thought — the Pharisees were Jewish Stoics and the Essenes resembled the Pythagoreans. He plays down bellicose messianism in order not to provoke Roman suspicions, blaming the war against Rome on a revolutionary minority. Josephus's reputation as an historian has noticeably improved in recent scholarship. Fergus Millar, perhaps the greatest living Roman historian, wrote in the 1987 Journal of Jewish Studies that the Jewish Antiquities was "the most significant single work written in the Roman empire". 

The survival of Josephus's writings is due largely to the respect with which they were held by Christians because of the references to New Testament characters in the Antiquities. He almost enjoyed the dignity of a fifth evangelist and had a statue in Rome in the fourth century. By the Renaissance, some doubts began to surround the genuineness of the paragraph relative to Jesus — known as the Flavian Testimony (Testimonium Flavianum), or the Jesus notice of Flavius Josephus — yet in 1737, Josephus's translator, William Whiston, still defended his veracity. He quoted Joseph Justus Scaliger, the prince of 16th-century Humanism, for whom Josephus was "the most diligent and greatest lover of truth" who was "more safe to believe...than all the Greek and Latin writers". 

The critical revival since the 19th century brought about a shift of opinion among leading scholars, tending towards the denial of the authenticity of the Jesus notice, and less frequently of those about John the Baptist and James. Nowadays, opinions are divided. Hence the question must be asked: Are the three notices the work of Josephus, or have they, or some of them, been produced wholly or partly by a Christian forger?