To understand the initial genetic changes that result in the formation of new species, we need to study species in the earliest stages of divergence. Drosophila athabasca is comprised of three closely related semispecies that differ dramatically in male courtship song and these song differences result in strong reproductive isolation among sympatric semispecies. To identify the genomic regions that are associated with these differences in song, we created a high resolution genetic map of D. athabasca using low coverage whole genome sequecing of F5 individuals. Our results provide important insights into the relative roles of the autosomes and sex chromosomes in the evolution of D. athabasca male courtship song differences and help identify regions of the genome that have promoted the evolution of behavioral isolation in this group.