Phylogenetic variation, recombination rate evolution, and comparative genome structure and organization have typically been explored in isolation. The chromosomal and genomic context of selected genetic markers in phylogenetic studies is usually unknown, given the fragmented nature of most genome assemblies. It is now established that the position of markers in the genome can strongly influence the inferred phylogeny, often not reflecting speciation patterns and subsequent bifurcating tree structure but rather post-speciation introgression. The recent availability of chromosome-level genome assemblies and advances in estimating genome-wide recombination rates have created opportunities to jointly understand the interplay of chromosome evolution, the landscape of recombination, and phylogenetic signal.