Equalization of parental contributions is one of the most simple and widely recognized methods to maintain genetic diversity in conservation programs, as it halves the rate of increase in inbreeding and genetic drift. It has, however, the negative side effect of implying a reduced intensity of natural selection so that deleterious genes are less efficiently removed from the population with possible negative consequences on the reproductive capacity of the individuals. Theoretical results suggest that the lower fitness resulting from equalization of family sizes relative to that for free contribution schemes is expected to be substantial only for relatively large population sizes and after many generations. We present a long-term experiment with Drosophila melanogaster, comparing the fitness performance of lines maintained with equalization of contributions (EC) and others maintained with no management (NM), allowing for free matings and contributions from parents. Two (five) replicates of size N ¼ 100 (20) individuals of each type of line were maintained for 38 generations. As expected, EC lines retained higher gene diversity and allelic richness for four microsatellite markers and a higher heritability for sternopleural bristle number. Measures of life-history traits, such as egg-to-adult viability, mating success, and global fitness declined with generations, but no significant differences were observed between EC and NM lines. Our results, therefore, provide no evidence to suggest that equalization of family sizes entails a disadvantage on the reproductive capacity of conserved populations in comparison with no management procedures, even after long periods of captivity.