The islands of eastern Indonesia occupy the major zone of contact and overlap between the reptile faunas of the Asian and Australo–Papuan regions. A survey of reptiles on twenty-eight islands in eastern Indonesia between 1988 and 1993 has documented several major range extensions and many new records of species on islands. The zoogeographic affinities of the snakes of Indonesian islands are re-examined in the light of both recent surveys and taxonomic research and coupled with that published previously. The major boundary in the snake fauna of Indonesia occurs between Sulawesi and the Lesser Sunda islands to the west and the northern and southern Maluku group of islands to the east; it corresponds to the major biogeographic boundary known as Weber's Line. The biogeographic affinities of the snakes of the Tanimbar islands are equivocal. The snake fauna of islands within the Lesser Sunda group indicate that separation between islands during the Pleistocene played a role in determining current assemblages and variation within species The islands of eastern Indonesia form biogeographic subregions that have relatively high levels of endemism and evidence of incipient speciation as a consequence of changes in sea-levels and climate during the Pleistocene.