Large-scale phylogeographical patterns and the underlying factors driving species divergence in Mesoamerica are poorly understood, but it is widely documented that tectonic events and Pleistocene climate changes play an important role in determining species diversification. As glaciations in Mesoamerica developed only around high mountains, one hypothesis is that the known effects of the Last Glacial Maximum on the geographical distribution and genetic diversity of bird populations, producing the contraction/ expansion latitudinal pattern observed in temperate bird species, should be largely undetected in resident bird populations inhabiting environmentally more stable habitats. To gain insight into the effects of Quaternary habitat and climate stability on the genetic diversity, we use ecological niche modelling and generalised linear modelling to determine the role of changes in habitat stability on the genetic diversity in eight widespread or range restricted hummingbird species. We found lesser changes in suitable habitat from past to present in most of the species than those predicted by palaeodistribution models at northern temperate regions. Contemporary seasonal precipitation, Quaternary habitat and climate stability had superior explanatory power, but the magnitude and directionality of their effects on genetic diversity varied between range-restricted and widely distributed species. We observed that the species studied have not responded equally to changes in climate stability in this complex region, suggesting that habitat differences and/or the altitudinal range of the hummingbird species influenced genetic diversity, and that the species-specific responses are not only linked to habitat stability in the region but also to contemporary seasonality associated with the availability of floral resources.