Neotropical humid montane forest (HMF) is divided by landform discontinuities which could limit gene flow among populations. The northern Andes is a complex montane system and an excellent region to compare the role of discontinuities dividing HMFs on the phylogeography of bird species. We study phylogeographic patterns of seven HMF bird species in the western slope of the eastern Cordillera to test whether the phylogeographic structure coincides with the presence of two landform discontinuities. We sequenced and analyzed a mitochondrial DNA locus from individuals collected in localities on both sides of the xeric ecosystems of the Chicamocha River Canyon and on both sides of the depression below 2000 m a.s.l. that separates the mountain range of Serranía de los Yariguies from the rest of the eastern Cordillera. Despite the low sample size for some species in particular localities, our results show that the major phylogeographic structure within most species (i.e. Adelomyia melanogenys, Henicorhina leucophrys, Basileuterus tristriatus, and Mionectes olivaceus) is located between both sides of the canyon. However, there is no phylogeographic structure in Doryfera ludovicae, Premnoplex brunnescens, and Arremon brunneinucha, despite some degree of genetic structure in the last two. Our results support a role of the Chicamocha River Canyon as a barrier diminishing, or precluding, gene flow. Evidence of gene flow between populations separated by the landform discontinuity between Serranía de los Yariguies and the rest of the eastern Cordillera indicates that it is not a barrier for most of the species, but could be a barrier to A. melanogenys that exhibits a different phylogeographic pattern. For this hummingbird, the haplotype of the Serranía de los Yariguies is related to haplotypes in other HMFs far away from the study region. Altitudinal changes of the HMF due to paleoclimatic changes are considered to explain the phylogeographic patterns of the species.