Silicateins found in spicules of siliceous sponges are proteins that take part in biogenic silica pre-cipitation and determine the morphological features of spicules. The exon-intron structure of the genes encoding four silicatein- isoforms (- 1, - 2, - 3, and - 4) from an endemic Baikalian sponge Lubomirskia baicalensis was studied. For eight sponge species, including both cosmopolitan (Spongilla lacustris, Ephydatia muelleri, E. fluviatilis) and endemic Baikalian (L. baicalensis, L. incrustans, Baikalospongia intermedia, B.fungiformis, Sw. papyracea) species, seventeen partial sequences of different silicatein isoform genes were determined. It was shown that cosmopolitan and endemic Baikalian sponges differ from each other in gene structure, in particular, in intron length. Among Baikalian sponges, silicatein- 1 genes had the highest variation of intron length, and silicatein- 4 genes were the most conservative. A phylogenetic analysis based on amino acid sequences of different silicatein isoforms identified four distinct clusters within the freshwater sponge clade. An analysis based on exon-intron gene sequences enables discrimination between different sponge species within the clusters.