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Abstract Comparative genomic analyses among closely related species provide an opportunity to assess their evolutionary history. The relatedness between species can depend on a variety of factors, including reproductive isolation, introgression, and incomplete lineage sorting, and this can impact divergence across the genome. Here, we use a combination of long- and short-read sequencing and HI-C scaffolding to assemble genomes for each of the four species in the testacea species group of Drosophila, including D. testacea, D. orientacea, D. neotestacea, and D. putrida, and its outgroup, D. bizonata. First, among species, we find many structural rearrangements across the genome as well as a large size difference in the dot chromosome that we infer is due to the expansion of repetitive elements. Second, we assess phylogenetic discordance and uncover a difference in the phylogeny inferred from genes on Muller E and the mitogenome relative to the rest of the genome, which may be due to recent hybridization. Lastly, we assess the rate of molecular evolution of genes shared across all species and identify genes evolving at different rates across the phylogeny. Our results present genomic resources for this species group and begin to probe into some of the evolutionary characteristics that contribute to variation in genome structure, while highlighting the need for high-quality genome resources to fully capture and understand the evolutionary history among closely related species.