Anopheles albimanus is a major malaria mosquito vector in Colombia. In the present study, wing variability (size and shape) in An. albimanus populations from Colombian Maracaibo and Chocó bio-geographical eco-regions and the relationship of these phenotypic traits with environmental factors were evaluated. Microsatellite and morphometric data facilitated a comparison of the genetic and phenetic structure of this species. Wing size was influenced by elevation and relative humidity, whereas wing shape was affected by these two variables and also by rainfall, latitude, temperature and eco-region. Significant differences in mean shape between populations and eco-regions were detected, but they were smaller than those at the intra-population level. Correct assignment based on wing shape was low at the population level (<58%) and only slightly higher (>70%) at the eco-regional level, supporting the low population structure inferred from microsatellite data. Wing size was similar among populations with no significant differences between eco-regions. Population relationships in the genetic tree did not agree with those from the morphometric data; however, both datasets consistently reinforced a panmictic population of An. albimanus. Overall, site-specific population differentiation is not strongly supported by wing traits or genotypic data. We hypothesize that the metapopulation structure of An. albimanus throughout these Colombian eco-regions is favoring plasticity in wing traits, a relevant characteristic of species living under variable environmental conditions and colonizing new habitats.