Omul, Coregonus autumnalis, are a commercially important coregonine fish from Lake Baikal, Siberia, Russia. In Lake Baikal, three morphotypes recognized by fishery experts occupy different zones in the lake: they are referred to as "littoral," "pelagic," and "benthic". Expressed character divergence was supported by whole-body morphometric analysis, but it is not known whether discrete genetic differences accompany the observed morphological variation. This study was designed to assess the genetic variation of three different omul morphotypes sampled from different locations in Lake Baikal that were segregated by morphotype in multivariate analysis. We surveyed genetic variation with restriction fragment length polymorphism analysis of specific gene loci amplified with the polymerase chain reaction. Sequence variation was localized in the mitochondrial control region. Though no discrete genetic markers were found, there is evidence of reproductive segregation by geographic location that corroborates geographic variation in morphological characters.