In the present study, we used morphological and behavioral analyses to assess the effects of seasonality and morphoclimatic patterns on the morphology, behavior, and distribution of 71 colonies of Africanized honey bees in 3 distinct ecoregions (Zona da Mata, Agreste, and Sertão) within the State of Sergipe, north-eastern Brazil. We found a high rate of gene flow among the studied colonies. However, there were pronounced morphological differences among localities and ecoregions, and body shape (r = 0.06239; P = 0.05) and size (P < 0.001) varied with altitude. Regional groups were separated by phenotypic plasticity, rather than genetic divergence. We also found a significant difference in the hygienic behavior of these populations between the dry and rainy seasons (P = 0.022; α = 0.05) and between ecoregions (P = 0.001; α = 0.05). The main modulator of hygienic behavior was the influence of temperature (ρ = 0.065; P = 0.471; α = 0.05) and altitude (ρ = -0.294; P = 0.001; α = 0.05) on rainfall (ρ = 0.274; P = 0.002; α = 0.05). This supports the hypothesis that environmental factors influence the expression of hygienic behavior trait. The influence of environmental factors on the morphology, behavior, and distribution of Africanized honey bees, together with the identified polyphenisms, indicate high genetic variability within these populations that can be exploited in future bee handling and breeding programs.