The evolution of animal genitalia has gained renewed interest, because of their potential roles during sexual selection and early stages of species formation. Although central to understanding the evolutionary process, knowledge of the genetic basis of natural variation in genital morphology is limited to a very few species. Using an out-bred cross between phylogenetically distinct lines of Drosophila montana, we characterized quantitative trait loci (QTLs) affecting the size and shape of the distiphallus, a prominent part of the male intromittent organ. Our microsatellite-based linkage analysis shows that intra-specific variation of the distiphallus involves several QTLs of largely additive effect and that a highly significant QTL co-localizes with the same inversion where we have earlier localized a large QTL for a sexually selected courtship song trait. The latter indicates that inversions can play an important role in shaping the evolution of rapidly evolving traits with a potential influence on speciation.