One of the largest beetles of Patagonia, Baripus (Cardiophthalmus), includes 20 currently described species. Its distribution ranges from the tip of Patagonia, on Tierra del Fuego Island, to isolated patches along the Andes and Extrandes mountains in northern Patagonia on the Payunia at >3,000 m elevation. Here, using RADseq data, evidence is found of mixed ancestry in different lineages. Phylogenetic network reconstruction shows two hybridizing edges between lowland and highland species. Using environmental niche modeling, we show changes in geographic distribution of potential niches of species during the last glacial maximum compared to their present distribution. Increasing potential niche overlap among different species pairs possibly explains how lineages came into secondary contact, supporting the hypothesis of hybridization. In addition, morphological evolution is studied using geometric morphometrics on the network and evidence of transgressive evolution has been found involving the pronotum shape, as well as highland/lowland habitat preferences. Finally, based on genomics and morphological data and using an integrative coalescent-based species delimitation approach, the separate evolution of two lineages in the early stages of speciation is found. Taken together, the dynamics of diversification of Baripus beetles in both space and time are discussed.