Sample of Gobio gobio from 30 localities in the Czech Republic and Slovak Republic were studied. Starch gel electrophoresis was used for evaluation of variability of allozyme patterns in 16 active protein systems comprising 26 loci. Products of 17 loci were considered to study the genetic structure of its populations. From this, genetic variability was found in ten loci, occurrence of rare alleles was detected in next four loci. Percentage of polymorphic loci ranged between 6 and 41%; mean occurrence of alleles was between 1.1 and 2.0 per locus; and mean heterozygosity was observed at 0.013 to 0.248. The genetic distances among populations were 0.002 to 0.175 (N e i 1972) and 0.063 to 0.385 (C a v a l l i - S f o r z a & E d w a r d s 1967). Differences in occurrence and frequencies of alleles in some loci among the sea basins were evident. Higher genetic variability identified in populations from the Danube river system (Black See basin) is probably connected with the fact that this basin served as a refuge for ichthyofauna during glaciations.