Abstract: Many bird species are specialized to live in the broadleaved, evergreen forests in the mountain regions in Southeast Asia. These mountain habitats are not continuously distributed as the different mountain areas are separated by lowlands, which has restricted gene flow and thus contributed to the high biological diversity in this region. The degree of connectivity between mountain areas has fluctuated with the Pleistocene glacial cycles, being largest during the glaciations when the mountain forests spread to lower elevations. Here we study how the intermittent periods of restricted gene flow and connectivity between the populations of five montane species of babblers (Aves, Timaliidae) in Vietnam may be traced in their genomes. The results suggest that the babbler species in the Central Highlands have been isolated from their sister-populations in northern Vietnam for between ca. 585 and 380 ky. For two species with populations in both the Central Highlands and the Da Lat region, we found that these split at more or less the same time (440–340 kya). We also found a significant statistical correlation between the time of the splits of these populations and the lowest altitude at which they are known to occur (no similar correlation was found with the geographic distances between populations). The populations in northern Vietnam show higher genetic variation than their counterparts in South-Central Vietnam, supporting the postulate that smaller populations may have lower genetic variation than larger. In accordance with this, we found the lowest genetic variation in the two species with the smallest populations in the Central Highlands. These two populations also show low levels of genomic heterozygosity. Our results show that the south-central populations of the studied babbler species are genetically distinct from their sister-populations in northern Vietnam, providing additional argument for the long-term protection of the evergreen mountain forests in Southeast Asia.