The vendace (Coregonus albula L.) inhabits several Latvian lakes. In Latvia this species is included into the list of specially protected species with limited use. Taking into consideration the high variability of vendace and the fact that it belongs to valuable and marketable fish, there arises a scientific interest to reveal possible reasons influencing its variability. There is no precise scientific data on the local vendace populations and its biology and this hampers the rational usage of this fish and possibilities of its reproduction in Latvian lakes.In the present work the genetic polymorphism and the structure of vendace populations in Rāznas, Nirzas and Sventes lakes in Latvia have been defined based on the analysis of isoenzyme systems and RAPD markers. The genetic variability and population structure both within and among vendace populations have been studied. The activity of eight isoenzyme systems was studied and 16 loci were selected for genetic analysis. Eight of them were polymorphic and used for the statistical analysis. Also, 60 decanucleotide (RAPD) primers were tested. For the analysis, eight decanucleotide primers were used.The average level of isoenzyme polymorphism in vendace populations from three lakes was 41.67%. The diversity of alleles based on allozyme data in the studied populations was approximately the same. Data of RAPD analysis showed that Coregonus albula populations from the studied lakes were highly polymorphic.The results of this study indicate that the estimated intraspecific variation may be more pronounced with RAPD markers than with allozymes when the two approaches were applied to the same populations.