Jean Yoyotte's teaching program at the Collège de France, which he unveiled in his inaugural lecture onMarch27 1992, is a continuation of his research into the geography of the Delta and the history of late Egypt. For six years, his lectures and seminars addressed subjects that had been little explored until then. Under the theme of " recherches de géographie historique et religieuse ", he analyzed the processions of " génies économiques " depicted in Greco-Roman temples, introduced little-known figures from the Egyptian pantheon and clarified the marginal functions of certain major gods. In particular, he continues the study of the Western Harpoon Province, ^VIIth  Nomeof Lower Egypt, which he began at the EPHE in 1988. Drawing on numerous iconographic and philological sources from the Ptolemaic period, and through a detailed prosopographical survey, he highlights the importance of the divinities and holy places in this poorly documented province on the north-western fringes of Egypt. In parallel, he devotes numerous sessions to " contacts between Egyptians and Greeks (^7th-2nd centuries BC) ", focusing on data relating to the town of Naucratis, known to be a Greekemporion on the canopic branch of the Nile west of the Delta. Choosing the title "  Naucratis, Egyptian city ", he refutes the idea of seeing this city as a " Greek enclave, isolated in its Hellenism and as if on the bangs of the Pharaonic universe ". While questioning the origin - Egyptian according to him - of the name Naucratis (Nȝy=w-Krḏ), he draws up a detailed assessment of the Pharaonic material on the site : documentation both epigraphic and archaeological that was hitherto little known to Egyptologists. He concludes that Naucratis was as much an Egyptian town as a Greek settlement, and assumes the existence of an initial temple toAmon-Ra-Baded on the site as early as the ^XXVIth Saite dynasty.

Between 1993 and 1995, he was invited to give a series of lectures in the Netherlands, Germany and France on the royal necropolis of Tanis, Egyptian-Greek relations and religious geography.

After his retirement in 1997, the professor, now an honorary member of the Collège de France, continued his work on the western Delta, adding important new contributions to his long list of publications. His research into religious geography also led him to take part in the work of the European Institute of Underwater Archaeology (IEASM) in the Bay of Aboukir, where he was responsible for analyzing material discovered at the site of the ancient cities of Thônis-Heracléion and Canope.