Diatom algae from six Pamir lakes located at an altitude from 3,729 to 4,213 m above the sea level were studied in 466 samples collected in summer period of 2000-2018. Altogether 300 species of diatom algae (330 with infraspecies) of 76 genera were revealed in periphytonic 466. The richest communities were found in two freshwater lakes Turumtaykul with 171 species (184 taxa) and Rangkul with 162 species (176 taxa). Floristic analysis with help of statistical methods show that the water salinity can be regulating factor of diatom diversity development in high mountain lakes. The Pinnularia genus was the richest in five from six lakes floras. The two floristic core were revealed in the analysis of the species overlapping. The natural status of the protected high mountain lakes as a result of our analysis is indicates a high level of conservation of diversity in the territory of the Tajik National Park and the adjacent high-mountainous areas. Advanced statistical methods help us to characterize the stability of studied algal floras in protected high mountain lakes as higher on the genera level then on the species level, and therefore species of studied floras can be source of evolutionary speciation.