Brown trout,Salmo truttais 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 stocking practices 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 reciprocal crossbreeds. The number of alleles per locus ranged between 3 (Str73INRA) -24 (T3-13). Observed (H-O) and expected heterozygosity (H-E) was between 0.188 and 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 the eight most informative microsatellite marker to their parental pairs was 96.08% and that of 15 loci was 98.04%. Having more than eight markers boosted only 1.96% extra power of assignment. Meanwhile correct assignment rate of five 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 reciprocal crossbreeds. The findings obtained in the present study would also be useful for performance evaluation of stocked fish, detecting crossbreeds and examining introgression into natural populations.