Brown trout, Salmo trutta is a widespread fish species throughout the Europe yet most of the natural populations of the species is in decline due to the anthropogenic pressures. Hatchery based stock enhancement is commonly used to restore depleted populations. Tracking pedigree information is useful for evaluating performance of stocked offspring and for examining introgression where hatchery-based stocking programs are being implemented. In this study, parentage assignment powers of 16 previously developed microsatellite markers have been evaluated in four brown trout strains and their hybrids. The number of alleles per locus ranged between 3 (Str73INRA) -24 (T3-13). Observed (H_O) and expected heterozygosity H_E were between 0.188-0.854 and 0.175-0.903, respectively. According to the simulation analysis with prior known parental and filial information, of the 204 offspring tested, correct assignment rate of 8 most informative microsatellite marker to their parental pairs was 96.08% and that of 15 loci was 98.04%. Having more than 8 markers boosted only 1.96% extra power of assignment. Meanwhile correct assignment rate of 5 loci was resulted only 85.29%. Our results demonstrate that microsatellite markers are reliable and effective tools for the parentage assignment in brown trout strains and their hybrids. The findings obtained in the present study also indicates that parentage assignment in brown trout strains would be useful for examining introgression into natural populations or to evaluate performance of stocked fish.