How do new species arise and diverge? Has been a fundamental question in evolutionary biology. The process of species divergence can be studied at many different levels of biological organization. However, it is until the recent advancements of genome sequencing technologies that genome-wide signatures of species divergence have started to unveil the complex genomic landscape of speciation. In this dissertation we investigate the landscape of genomic divergence using a classic pair of Drosophila species. We generated four new high quality genome assemblies for Drosophila pseudoobscura and D. persimilis to explore the genomic differences at three different levels. We first characterized the structural variation landscape between D. pseudoobscura and D. persimilis and stablished its association with transposable elements and tested how intrinsic genomic factors, such as recombination, influence the accumulation ofstructural variation associated with transposable elements in both species. With a combination of high-quality genome assemblies and a comprehensive population genomics data set, we also explored how the contribution of recombination rate and introgression promote sequence divergence with the potential of forming species barriers. Moreover, we investigated how gene co-expression networks potentially rewiring between species contribute to the divergence landscape between D. pseudoobscura and D. persimilis. Our work highlights the complex landscape of species divergence occurring at multiple levels of organization. Moreover, the integration of potential species drivers identified at different scales shed lights on the molecular mechanisms involved in speciation.