The RFLPs detected by the AvaII, BamHI, EcoRV, KpnI, HaeIII, and RsaI restriction enzymes in the D-loop region of mitochondrial DNA of the Northern Selkups were analyzed. Frequencies of the rare variants were estimated for all polymorphic sites examined. A total of 16 mitotypes were described. Results were compared with the literature data on mitochondrial DNA polymorphism in Caucasoid and Mongoloid populations. High frequency of the KpnI bp 16129 site loss (28.14%) together with a remarkably reduced number of mitotypes in the group of variants with the frequency of 2% compared to the Russians and Mongols, was considered to be the most informative population feature of the Northern Selkups. All variants found in the Selkups, occurred more frequently in the Mongols than in Russians. Four out of ten rare variants (frequency < 2%) observed in the Selkups were detected in Mongols and Russians. The frequency of three of these variants was higher in the Russian population. Six mitotypes were characterized as Selkup-specific. These observations suggest a considerable reduction of mitochondrial gene pool diversity in Northern Selkups compared to larger ethnic groups of Mongoloids and Caucasoids. The structure of mitochondrial genome in Selkups is defined by the presence of the major Mongoloid and minor Caucasoid components, which suggests complex ethnogeny of the contemporary Selkup population.