The genetics of sexual isolation, behavioral differences between species that prevent mating, is understood poorly. Pheromonal differences between species can influence sexual isolation in many animals and in some cases a single locus can cause large functional changes in pheromonal mating signals. Drosophila cuticular hydrocarbons (CHCs) can function as pheromones and consequently affect mate recognition. In a previous study of the two major CHCs in females that affect mating discrimination between Drosophila simulans and D. sechellia, quantitative trait loci (QTL) were identified on the X and third chromosome, and a few candidate genes were potentially implicated. Here we specifically test candidate genes for CHC biosynthesis and determine the genetic architecture of four additional CHCs that differ in abundance between D. simulans and D. sechellia females. The same QTL, and new ones, were found for additional CHCs. By examining all these CHCs and exploring their covariance, we were able to ascribe putative function to the major QTL. Although desaturases have received considerable attention for their role in CHC biosynthesis, evidence here implies that elongases may be just as important. Sex determination genes do not seem to have a role in this species difference although D. sechellia is sexually dimorphic in CHCs, whereas D. simulans is not. Epistatic interactions, only detected for CHCs limited to D. sechellia, imply that complex interactions among loci may also be having a role in these compounds that affect mating isolation.