High diversity of silica-scaled chrysophytes was recorded in the Barguzin River mouth and the Selenga River delta. Their flora was represented by 66 species and intra-specific taxa: Chrysosphaerella — 2, Paraphysomonas — 8, Clathromonas — 5, Spiniferomonas — 8, Mallomonas — 29, and Synura — 14. Eight taxa of silica-scaled chrysophytes were observed for the first time in Russia: Chrysosphaerella rotundata, Mallomonas doignonii, M. trummensis, M. corymbosa, Clathromonas poteriophora, Paraphysomonas acuminata acuminata, P. vulgaris, and Synura laticarina. In May, we found scales of Mallomonas striata with morphologically changed structure in the mouth of the Barguzin River and Srednyaya Channel of the Selenga River delta. The flora of silica-scaled chrysophytes studied differs from one tributary to another. We observed only 52 species in the Selenga River delta, whereas in the Barguzin River mouth we identified 35 species. These large rivers affect the flora of Lake Baikal diversifying silica-scaled chrysophytes in its southern and central basins. The total list of species and intra-specific taxa in the Selenga River delta, Barguzin River mouth, and in Lake Baikal includes 72 taxa. Therefore, this area may be considered as a “hotspot” of silica-scaled chrysophytes together with three hotspots observed worldwide earlier.