Most characters affecting morphological divergence between taxa are likely to have a complex genetic architecture, with multiple interacting genes contributing to the observed phenotype. The morphological characters that discriminate among taxa often vary continuously within taxa. One can begin to understand the genetic basis of morphological evolution by mapping the quantitative trait loci (QTL) affecting within-species variation for the traits of interest to the level of genetic locus, and determining the effects of the QTL. Recent progress towards this goal has been made using Drosophila sensory bristle number as a model system. Drosophila bristle number QTL have been mapped by linkage to polymorphic retrotransposable element markers in recombinant inbred lines derived from strains with highly divergent bristle numbers, and from strains that were not selected for bristle number. The effects of bristle number QTL range from very large to the smallest effect detectable given the experimental sample sizes. The effects of bristle number QTL are often sex- and environment- specific, and QTL interact epistatically. The chromosomal locations of bristle number QTL determined from independent parental strains often coincide, suggesting that the same loci cause variation for these traits in many geographic populations. Further, the QTL map positions are often consistent with the map positions of candidate genes affecting bristle development. Fine-scale introgressions of six gene regions containing fifty naturally occurring alleles of candidate genes into a common inbred background, in conjunction with tests for quantitative complementation of the wild-derived alleles with mutant alleles of the candidate loci, support the hypothesis that the candidate loci harbor naturally occurring variation affecting bristle number. Tests for association of molecular variation at three candidate genes with phenotypic variation in bristle number within populations show that molecular polymorphisms in introns are in linkage disequilibrium with quantitative variation for these characters. Regulatory variation at key developmental loci may contribute to quantitative variation for morphological characters within populations, and by extension, to character divergence between species.