Ochlerotatus triseriatus is the natural vector of La Crosse virus, a common cause of pediatric encephalitis in the United States; the closely related Ochlerotatus hendersoni transmits this virus at low frequency. Adults of these mosquito species are difficult to distinguish morphologically; however, the larval stages show species-specific differences in several characters. We identified genomic regions contributing to the differences between the larvae of these species through interspecific hybridizations. Quantitative trait loci (QTL) were identified by standard interval mapping techniques and by univariate marker association analyses. We examined 159 F2 progeny from an Oc. hendersoni female by Oc. triseriatus male interspecific cross for variation in the number of saddle and siphon hair branches, attachment of the acus, and morphology of the anal papillae. At least one putative QTL was identified for each of the phenotypes examined. QTL most commonly mapped to linkage group (LG) III, although QTL were identified on LGI and LGII for three phenotypes each. Several of these QTL, and particularly those on LGIII, also map to genome regions controlling adult female body size and ability to orally transmit La Crosse virus. Further studies are required to elucidate the relationships among these traits and the impact they may have had on the ecological specialization and speciation of these mosquitoes.