Mangareva, along with several other islets from the ‘Gambier almost-atoll’, are residual parts of a past volcano pertaining to the Gambier Archipelago (South Pacific). The islets are surrounded by a vast lagoon delineated by a partly subsided coral barrier reef. Benthic diatom assemblages from these marine environments included, among others, Achnanthales and species of the elusive genus Olifantiella, with Cocconeis, Amphicocconeis and Planothidium as the most diverse genera. Hao, a large Tuamotu atoll 830 km northwest of Gambier, was sampled at about the same time. A Non-Metric Multidimensional Scaling applied to data from Mangareva and Hao highlighted groups of locations and biotopes. A PERMANOVA analysis was applied to test for the effect of both biotope and location on the differences in community composition. The geologic history of the reef structure (from volcanic and silicic environments surrounded by a reef in Mangareva, to typically coral and calcic environments in Hao, with a much older geologic history) may have played a role in the degree of colonization by benthic diatoms. Some taxa and morphs were only observed in Mangareva, whereas some others, present in north Tuamotu, were apparently absent in Gambier, permitting some remarks on tropical diatom biogeography and possible endemism, taking into account that the Gambier sector is located to the south in the South Equatorial Current, and thus largely removed from the influence of other Polynesian islands.