In southern regions of Western Siberia, Ixodes persulcatus ticks co-exist with Ixodes pavlovskyi. Both tick species have similar morphology, and natural hybridization of I. persulcatus and I. pavlovskyi ticks has been observed. To investigate the role of I. pavlovskyi ticks and I. persulcatus/I. pavlovskyi hybrids as vectors, correct identification of tick species is necessary. The nuclear crt gene might be useful in distinguishing I. persulcatus from I. pavlovskyi ticks. Genetic variability in this gene has been studied and substantial differences between crt gene sequences of I. persulcatus and I. pavlovskyi ticks has been demonstrated. In this study, maximum-likelihood analysis showed that sequences of I. persulcatus and I. pavlovskyi ticks were identical or highly homologous among themselves. These results were confirmed by a Bayesian phylogeny. We conclude that crt gene sequences of I. persulcatus and I. pavlovskyi cannot be used for distinguishing these tick species and that the conflicting results of prior studies reflect samples from incorrectly identified ticks rather than real genetic differences between I. persulcatus and I. pavlovskyi.