Abstract <p>The 18S metabarcoding technique was used to characterize the genetic diversity of <i>Chlorophyta</i> microalgae in geographically remote hypersaline water bodies in the European Russia. At high taxonomic levels, stronger salinity was associated with lower diversity of <i>Chlorophyta</i>; however, this pattern was disrupted at the phylotype level due to significant genetic diversity of the genus <i>Dunaliella</i> and related taxa. The presence of phylotypes unidentified at the genus level and related not only to halophilic species but also to marine and freshwater ones indicates that communities of green microalgae in hypersaline conditions have been studied insufficiently to date. Most water bodies studied had unique sets of dominant phylotypes that were determined by salinity, as well as by other factors. A salinity threshold of 110‰ was estimated as the boundary discriminating <i>Chlorophyta</i> communities in terms of structure and diversity.</p>