The genetic variability of burbot (Lota lota L., 1758) inhabiting the Ob-Irtysh and Taz river basins in Western Siberia has been studied based on the polymorphism of the hypervariable fragment of mtDNA control region (407 bp). The analysis of 134 fish samples revealed 30 haplotypes, 23 of which were new. Among haplotypes, previously detected in Eurasia and North America, EB30 was the most frequently found in Western Siberia (45.5% frequency). The results of our study are in agreement with previous research pointing to the genetic differentiation of two burbot subspecies, L. l. lota and L. l. maculosa, and indicate that burbot inhabiting the Ob-Irtysh and Taz river basins belong to the Eurasian-Beringian clade (nominative subspecies L. l. lota). However, a high genetic diversity of burbot in Western Siberia, along with a relatively high differentiation of burbot groups within studied territory, points to a regional specificity of burbot population.