This paper reports on a new species of the Baikal endemic sponge (fam. Lubomirskiidae) Swartschewskia khanaevisp. nov. The description of this species is based on morphological and molecular data (ITS and mitochondrial IGRs). Morphologically, S. khanaevisp. nov. differs from S. papyracea by loose tracts arranged in an irregular network as well as the presence on strongyles of compound spines looking like tubercles densely ornamented with simple spines. Moreover, specimens of S. khanaevisp. nov. show a peculiar structure of the aquiferous system at the body surface that may be an adaptive trait for environmental conditions. Phylogenetic analysis has revealed that S. khanaevisp. nov. forms a well-supported (0.99) monophyletic clade with S. papyracea and is allocated as its sister taxa.