Common whitefish (Coregonus maraena) in Poland belongs to the endangered species. The degradation of the environment causes common whitefish to lose its natural reproduction sites. The natural genetic structure of whitefish has been compromised by anthropogenetic activities involving eutrophication, river regulation, the introduction of non-native species and as well as excessive exploitation of the species. The genetic variability of common whitefish (Coregonus maraena) from 2 sites: Pomeranian Bay and the lower Oder river, was assessed using microsatellite markers. A total of 45 caught individuals were analysed (26 from Pomeranian Bay and 19 from the Oder river). Polymorphism at nine loci, Str60INRA, Str73INRA, Strutta 12, OmyFgt1TUF, Str85INRA, Str591INRA, Ssa85, Ssa197, T3-13 was assessed. The results indicated that all the investigated populations showed a high level of genetic variability. The level of genetic variability was determined using the FST parameter and was high investigated populations (0.215). Microsatellite analysis demonstrated a higher observed heterozygosity as compared with the expected heterozygosity in all the investigated populations. The FIS coefficient values below zero in all the investigated populations of common whitefish indicate the excess of heterozygotes. The high number of heterozygotes may be related with a more intense influx of genes from outside of the local population. The study demonstrated that microsatellite markers (SSR) are very useful in the assessment of the genetic variability of common whitefish (Coregonus maraena). Our results characterize the selected populations of whitefish and may be useful for further research on this endangered species.