Covariation patterns of dental traits vary greatly among mammals due to the effect of evolutionary factors. Studies of integration and modularity in dentition in closely related species could provide insights into evolutionary patterns at higher taxonomic levels. We studied the initial stage of trait divergence using two subspecies of closely related bat species, Myotis myotis myotis and M. blythii oxygnathus (family Vespertilionidae), utilizing a collection of 105 specimens from Ukraine and 63 paired quantitative characters. We identified modularities in the dentitions. For vestigial teeth, we found decreased correlations with other teeth and increased variation. The overall modularity of odontometric characters was slightly higher in M. b. oxygnathus. The internal constraints on evolutionary change were unexpectedly high. Variation and covariation in tooth sizes were critically limited in the studied Myotis species, which could be attributed to the need to maintain accurate occlusion. Using the example of M. myotis and M. blythii dentition, we observe the initial stage of the divergence in a highly canalized structure.