To compare the level of mitochondrial divergence between avian populations east and west of the open vegetation corridor (OVC), an environmental barrier that currently isolates the Atlantic Forest from the Andean forests and Amazonia, and assess whether biological attributes can explain the patterns of intraspecific variation observed. We estimated net genetic divergence between populations on opposite sides of the OVC for 71 bird species based on 727 sequences of the mitochondrial gene COI. Species were categorized based on three ecological attributes and two morphological traits. The relationship between divergence and the biological attributes was assessed through generalized linear mixed models and univariate analyses. Divergence between populations on both sides of the OVC tended to be low, implying that nearly all diversification events took place within the Pleistocene, and discordant among species. Differences in habitat specialization were by far the most relevant to explain this discordance, with significantly higher intraspecific distance among forest specialists than among species capable of inhabiting open environments. The relative importance of all other traits was notably lower, but understory species that feed on animals showed a significantly higher genetic divergence across the OVC than those with a plant-based diet that forage in the canopy. We found no association between genetic distance and morphology. Ecological attributes can explain the pattern of discordant mitochondrial divergences between populations on both sides of the OVC. Our findings emphasize the need for more comparative studies that take into account functional traits.