The brown trout (Salmo trutta) is an ecologically, economically, aesthetically fish species whose poor conservation status in the European countries calls for further attention and action. The continuing erosion of the genetic resources of brown trout populations by human activities calls for strategies to reverse the current trend. We studied a genetic diversity of population of brown trout in the territory of Czech R. and in Slovakia using genetic markers. In the fragments of mitochondrial DNA (gen for ND-5/6) and nuclear DNA (gen for LDH1) amplified through PCR the differences were searched with the use of RFLP. In tested populations seven haplotypes were founded, four haplotypes were represented in almost of all populations. The ``Danubian haplotypes{\crqq} were strictly confined to the Danubian and Vistula drainages, the ``Atlantic haplotypes{\crqq} dominated in all populations, most of the total molecular variance (72 %) was attributed to differences within populations. Two alleles at LDHC1٭ - the ancestral ٭100 and ٭90 (at a high frequency) were revealed. This genotypic replacement is considered to be due to anthropogenic activities.