Morphology-based identification and classification of sponge species is complicated, because their morphological features are highly variable. Therefore, molecular markers are ideal tools for delimiting sponge species. In this study, we compared the variability of two sections of COI (the standard 5'-end fragment and the I3-M11 fragment) for closely related Baikal sponge species. Although the mean interspecific variability for both fragments was higher than the mean intraspecies divergence, these values overlapped in some cases. Based on the results of the study, we concluded that the I3-M11 fragment and the standard 5'-end fragment were not suitable when used in the canonical fashion for identifying Baikal species. However, the consistency in differences between lineages in number of non-synonymous substitutions of the two investigated COI fragments indicated that nucleotide substitutions in the I3-M11 fragment of COI are evolutionarily more informative for delimiting species. We also detected new divergent haplotypes of Baikal sponges using these markers. Seven new haplotypes in the standard 5'-end fragment of COI and 10 in the I3-M11 fragment were observed. These findings potentially indicate cryptic speciation in Baikal sponges, and further study is required to elucidate how this cryptic speciation evolved.