Molecular data allows us to disentangle the phylogenetic relationships between species. Through genetic analyses, we have gained a better understanding of the speciation process, the prevalence of hybridization between sister taxa, and how mammalian lineage diversification occurs through time. Nevertheless, some mammalian taxa have complex evolutionary trajectories, and, in many cases, traditional molecular markers have not been able to provide good phylogenetic resolution. Phylogenomic approaches based on mitogenomes and whole genome sequencing (WGS) are powerful tools, as thousands of loci provide stronger statistical support to phylogenetic relationships, but also uncover hybridization or introgression events. In this chapter, we review the contribution of genomics to phylogenetic analysis in advancing our understanding of the processes of speciation and diversification, with some examples of its application for the study of the speciation and diversification of Neotropical mammals.