To collect information on possible impacts of a nuclear power plant on the formation of the genetic structure of the population of perch as an intensively exploited fish species, an investigation into the scope of intraspecific genetic diversity of a rapidly changing mtDNA D-loop region of perch was initiated. We determined the partial D-loop sequences for 173 perch specimens representing populations of Drūkšiai, Plateliai and Metelys lakes as well as Nemunas Delta, Neris River, Curonian Lagoon and Baltic Sea coastal area. A total of 22 different haplotypes of which 12 could be found only in perch populations dwelling in Lithuania were determined. It should be noted that the Lake Drūkšiai perch population distinguished by abundance of unique haplotypes: of eight determined haplotypes four were characteristic only of this particular water body. In a neighbour-joining tree constructed based on K XY coefficients, inter-populational perch phylogenetic relationships were disclosed and close genetic relationships of the population of Lake Drūkšiai with the Neris River perch population were determined. Analysis of frequencies of haplotypes assigned to different haplogroups confirmed the uniqueness of the genetic structure of the perch population of Lake Drūkšiai.