The Andes are an example of how geographical events, climatic and ecological conditions drive speciation and evolution of species. However, the processes leading to this diversity, such as the relationships between related lineages, are still poorly understood. Studying the phylogeography of endemic and widely distributed species in the Neotropical region is an effective method to describe the evolutionary processes underlying the appearance and the maintenance of species. The two related lineages, Embiratermes neotenicus and its supposed sister species, E. chagresi (Termitidae: Syntermitinae), have been observed in sympatry in the west of the Andes although the literature suggests their geographic separation. To better understand the biogeographical processes and to gain insight into the evolutionary history of these species in this region, we collected the two termite species all around the sympatry zone (Panama, West and East Colombia, Ecuador) and analysed morphological features, mitochondrial (COI, COII, 16S) and nuclear (ITS2, Wg, microsatellite loci) DNA variation. We found mito-nuclear incongruences and admixed individuals in the sympatry zone and few morphometrical differences between lineages. Our analyses of the reproductive system suggest that E. chagresi is also able to reproduce through Asexual Queen Succession like E. neotenicus. We proposed that the two lineages diverged because of the Andes uplift and then reconnected due to climatic and geographic changes, northwestern Colombia being considered as a secondary contact zone.