One of the main goals in evolutionary biology is to understand speciation. By studying recently diverged populations of the fruit fly Drosophila athabasca, we aim to pinpoint the genetic causes for speciation phenotypes and gain an understanding of the genomic divergence in this species complex. The D. athabasca species complex, which consists of three behavioral species - West-Northern (WN), Eastern A (EA), and Eastern B (EB) - have diverged only in the last 5,000-16,000 years. In this short time frame, the three behavioral species have evolved near-complete sexual isolation due to rapid divergence in female mating preferences for different male courtship song. By taking advantage of the recent divergence times, in this study we used Next-Generation-Sequencing to study the genetic relationships between each behavioral species, assess how much genetic variation and differentiation exists within and between geographical populations of each species, and whether these sexually isolated species are presently exchanging gene flow in areas of sympatry. Our results provide novel insights into understanding how such rapid cases of speciation occur in nature.