Ixodes ricinus (Linnaeus 1758) and Ixodes persulcatus (Schulze 1930) ticks are involved in the transmission of a wide variety of pathogens with considerable impact on human and animal health. The co-distribution zone of these two tick species is situated in the Baltic countries, which provides a special setting for the population studies. In the present study, genetic variability of I. ricinus ticks collected in allopatric and sympatric locations in the Baltic countries has been investigated using a sequence analysis of the mitochondrial DNA control region, 16S rRNA and cytb genes. There were 32 haplotypes (Hd: 0.8551) and 27 haplotypes (Hd:0.8213) of control region sequences from ticks in allopatric and sympatric zones detected, respectively. Out of 47 16S rRNA gene haplotypes, 32 haplotypes (Hd: 0.7213) were found in the allopatric zone and 27 (Hd:0.9572) in the sympatric zone. The Cytb gene was very conserved and monomorphic in ticks from the allopatric zone, whereas three unique haplotypes were observed in the sympatric zone. The higher number of unique haplotypes of the control region was detected in the allopatric zone. Median joining network and Fst analysis did not reveal a clear separation between ticks from the two zones.