We present the results of the first ever research on biodiversity and biogeography of marine benthic diatoms from coral reefs of the tropical islands of Indonesia, including West Borneo, East Java, South Celebes, Komodo, Rinca and Flores. The sampled islands offer a broad range of coral reef microhabitats and host diatom assemblages from seaweeds, sea grass, dead corals, scrapes from other biological surfaces, sand, rocks and other solid surfaces. The results of this study are based on the light (LM) and scanning electron microscopy (SEM) identification of diatoms only. Our taxonomic analysis revealed the presence of 911 diatom taxa representing 188 genera. Biodiversity indices such as Shannon, Simpson and Evenness as well as species richness and diatom relative abundance were calculated for each sample examined. We find that these indices were higher for Indonesia than those published for tropical oceanic islands or regions from both hemispheres, e.g. Galapagos and Martinique, but comparable to Madagascar. The non-metric multidimensional analysis showed that the type of habitat from which a particular sample was taken was of greater significance in the taxonomic composition than the geographical aspect. In terms of biogeography, cosmopolitan taxa were dominant in terms of relative abundance, but species richness was higher within tropical zonal and local forms. Many taxa were identified only at the genus level, and may turn out to be new to science.