The identification of genes contributing to speciation has the potential to provide important insights into the mechanisms of evolution. One of the most interesting unresolved puzzles is the relationship between intraspecific variability in morphological traits and their interspecific divergence. Intraspecific polymorphisms without major detrimental side-effects may serve as a substrate for selection response during speciation. The same quantitative trait loci (QTLs) may, then, account for the trait variability both within and between species. In contrast, the vast majority of intraspecific variants could be deleterious mutations that have not yet been selected out. In this case intraspecific variation would not ultimately generate interspecific trait differences. In previous work, QTLs responsible for morphological differences between animal species, including those for the secondary sexual trait sex comb tooth number, have been mapped with the resolution of chromosome segments. Here, we mapped QTLs for which alleles segregated between two laboratory lines of Drosophila melanogaster. The two QTLs identified mapped to the X chromosome and accounted for only 8% of the between-line differences, implying that a large number of small-effect genes modify sex combs. One intraspecific QTL mapped to the same interval as the QTL for interspecific differences between D. simulans and D. mauritiana. Whether or not these effects result from the same genes requires further examination.