The evolution of late season reproductive arrest (diapause) among female Culex pipiens mosquitoes allows them to overwinter in temperate climates, while females of the sibling species Culex quinquefasciatus do not exhibit the diapause phenotype. We present results for quantitative trait loci (QTL) analyses of two independent segregating populations derived from crosses between C. pipiens and C. quinquefasciatus. QTL for diapause and three life history traits were identified and compared for genome positions and gene effects. Using a combination of composite interval mapping, single-marker analysis and all possible subsets regression, we identified multiple QTL for each trait, totalling 14 and 17 QTL for each population, respectively. Individual QTL across traits often mapped to similar genome locations, suggesting these traits may be controlled in part by genes with pleiotropic effects or multiple tightly linked genes. The majority of QTL were intermediate in magnitude in that they explained 10-25% of the phenotypic variation. The majority of QTL showed overdominance effects. We suggest that this could impact natural populations, as increased heterosis across hybrid zones may allow populations to adapt to environmental conditions via stabilizing selection, and yet maintain species identity outside these regions because of strong morphological integration, wherein related traits evolve as an integrated unit.