Sixteen isozyme systems were examined by starch gel electrophoresis in vendace, Coregonus albula L. Samples of muscle and liver were analysed from over 2000 fish representing 31 populations. A total of 41 loci were identified. Out of these, 33 appeared suitable for population genetic studies. Polymorphism was observed at 24 loci, of which 17 are described for the first time in vendace. In addition, new alleles are reported for four previously known loci. The average heterozygosity per individual per locus is 7.9%, and 42% of the loci are polymorphic. These values are relatively high for a salmonid. There is extensive genetic heterogeneity among populations. The variability patterns showed that 58% of vendace genes have retained duplicate gene expression. This was due to liver specific Gpi‐3, 4 and Me‐3, 4, which both were expressed as duplicates. In previous studies a single locus has been found coding for these enzymes in the liver‐specific zone of salmonids. The results throw light on salmonid evolution and management of vendace populations.