This study was undertaken to assess the feasibility of microsatellite markers for resolving parentage in Labeo rohita (rohu) selective breeding programmes in lieu of conventional PIT tag marking. Ten microsatellite markers were used to assign offspring parentage. A total of 160 individuals were tested from eight full-sibling families. Eight highly polymorphic loci with allele numbers ranging from 2 to 8 and polymorphism information content (PIC) values in the 0.47–0.82 range were utilized. With the use of a real data set from a breeding programme, all but 12 individuals out of 160 could be assigned exclusively to their correct parental pairs. The matching rate was 92.5%, which was lower than in a simulated study (98.44%, Excl-2). Discrepancies between simulations and real data sets may be due to several factors such as genetic relatedness among candidate parents (half-sib and full-sib), presence of null alleles, and sampling variance of the parents. The results of this study suggest that a marker panel probably with a wider genome coverage may be necessary for near-100% accuracy in assigning parentage in rohu selective breeding programmes.