Sexes often have differing, potentially conflicting fitness optima, resulting in intralocus sexual conflict, as each sex bears a genetic ‘load’ of the opposite sex. To understand conflict in the genome, one strategy is to artificially select a population discordantly, against established sexual dimorphism, to reintroduce an attenuated conflict. We investigate a long-term artificial selection experiment where sexual size dimorphism has been reversed inDrosophila melanogasterafter ∼350 generations of sexually discordant size selection. We explore morphological and genomic changes to identify loci between the sexes in discordantly and concordantly selected treatments. While concordant selection maintains ancestral sexual dimorphism, discordant selection responds in a trait-specific manner. We observe multiple, possible soft selective sweeps in the genome, with size related genes showing signs of selection. Patterns of genomic differentiation among the sexes within each lineage identified potential sites maintained by sexual conflict. One discordant selection lineage shows a pattern of elevated genomic differentiation (FST) on chromosome 3L, consistent with the presence of maintained sexual conflict in the genome. Our results demonstrate the polygenicity of body size, as well as sexual conflict. Furthermore, our results also suggest visible signs of conflict and differentially segregating alleles between the sexes due to discordant selection.