Due to the position of Colombia between Central and South America, and the presence of several ecosystems in its territory, phylogeographic information from populations across this country is fundamental to understand theevolutionary history of widespread Neotropical species. The Andes have long been noted for their influence isolating lowland species into cis- and trans-Andean populations. However, detailed sampling across cis-Andean zones adjacent to the Andes (i.e., Orinoquia) has been lacking in avian phylogeographic studies. Information from DNA sequences, from 2 passerine birds: Dendrocincla fuliginosa and Xenops minutus is presented herein; to depict their phylogeographic patterns, focusing on the relationship between cis- and trans-Andean populations from Colombia. The analyses, regardingColombian samples indicated that cis-Andean populations (i.e., Orinoquia and Amazon) are not closely related, rather the Orinoquia populations are more closely related to trans-Andean populations in both species. These relationshipssuggest that populations on both sides of the Andes were connected in the recent past (less than 1 myA). I propose that phylogeographic differentiation in lowland species in this region is not only explained by the presence of the Andean mountains, but also based on the ecological shifts between major ecosystems such as Amazonia and Orinoquia.