The diatom flora of the Falkland Islands was investigated by sampling twenty-eight representative lake, pond and stream habitats. Diatom assemblages were moderately diverse and dominated by benthic taxa characteristic of oligotrophic soft waters. Particularly the Fragilarioid and Achnanthoid taxa possessed unusually small valves and this condition is thought to be favoured by the prevailing harsh environmental conditions. Eleven new diatom taxa are described and several new combinations are proposed but it is likely that further research will show that at least some of the new taxa will co-occur, in Patagonia and elsewhere, rather than be endemic in the Falklands archipelago. Taxon richness varied strongly between sites but only weak trends were indicated between total number of taxa, number of regional endemic taxa, or rare taxa and habitat complexity, habitat size or water pH (diversity models were not used because dispersal and immigration rate data are lacking). Cosmopolitan taxa were most common but a significant portion (approximately one third) of the assessed flora was attributed to taxa with regionally restricted distributions. Southern South American, Subantarctic and North American elements were present but probably very few taxa are entirely restricted to the Falkland Islands. Macro- and microecological factors determine both the composition and numbers of taxa in a diatom sample. The species assemblages recorded are thought to reflect near pristine aquatic conditions at all the Falkland sites (palaeolimnogical techniques are nevertheless required to test hypotheses about native and non-native taxa). Irrespective of difficulties in fitting diatom data to species diversity models, the occurrence and abundance of diatom taxa in these representative samples provide a unique site-specific biological signature that reflects water quality and physical habitat as well as regional flora attributes. Routine diatom analysis for ecological purposes requires accurate taxonomy and consistency is of paramount importance but, compared with biogeographic and systematic studies, a lower level of precision is probably adequate. 8. Monitoring diatom communities offers one way of perceiving environmental change and global warming is thought to pose the greatest threat to the biological integrity of the inland waters of the Falkland Islands.