In the last decade, events of mass disease and mortality of sponges have been observed on Lake Baikal, which indicates an ecological crisis on the Lake. Based on the crucial role of sponges as filter feeders and bioindicators, their comprehensive study in this situation is of great interest. Despite the presence of genomic and transcriptome data for several species of endemic Baikal sponges, their population structure has never been studied before. The analysis of the population structure of both marine and freshwater sponges is successfully carried out using microsatellite markers. For freshwater sponges, the only species for which microsatellite markers have been pub lished is Ephydatia fluviatilis, a close relative of the Baikal endemic sponges. Microsatellite markers show a high percentage of interspecies cross-specificity among invertebrates. According to this, we attempted here to assess the suitability of these microsatellite markers for population genetic studies of endemic Baikal sponge Lubomirskia baikalensis based on genomic data. The presence of mi-crosatellite sequence markers homologous to the flanking regions in the L.baikalensis genome was shown for 63.6% of markers, 71.4% of which contained microsatellite sequences. However, all of these markers require the development of species-specific primer pairs.