Monitoring of the analysed populations of the endangered fish species Misgurnus fossilis was conducted using microsatellite analysis and sequencing of a part of the control region. Absolutely first microsatellite markers for weather loach were found. Six polymorphic microsatellite loci were prepared, five of which were tested. Number of alleles per a locus ranged from 3 to 5. All studied populations are differentiated one from another (FST= 0.205 - 0.367). All sampled populations contained unique alleles. Sequential analysis of the mitochondrial control region showed great haplotype similarity of the studied populations which come from one widely spread haplotype H_1, and thus suggested possible hypothesis of recent spreading from one source.