Despite the common geographic occurrence of inland (athalassic) saline habitats, their biota has not been extensively studied. Diatoms have been estimated to contribute as much as 25% to the earth's primary production (Werner, 1977). However, in hypersaline systems the proportion of in situ carbon fixation by diatoms is likely to be higher. We used substrate samples taken from the Salt Plains National Wildlife Refuge, an athalassic hypersaline ecosystem, to investigate the relationship between diatom genus diversity, composition and salinity. These samples range in salinity from 14 to 306 ppt and contain 21 genera. Six genera (Cymbella, Mastogloia, Psammodictyon, Amphora, Navicula and Nitzschia) comprise 97% of the diatoms counted in all samples. Diatom genus diversity shows an inverse relationship with salinity, while genus richness shows no clear relationship with salinity. Hence, loss in diversity is the result of dominance by fewer taxa at higher salinities. The relative abundance of the genus Navicula is positively correlated with salinity, with it dominating the highest salinity sites. We used a canonical correspondence analysis (CCA) to explore the relationship between salinity and relative abundance of diatom genera. The primary variables influencing diatom genus composition at the Salt Plains were found to be the variability of salinity within a site and the overall magnitude of salinity.