Investigating parallel roles of geography and environmental heterogeneity in diversification provides insights on how neutral and selective forces drive the evolution of biological systems. Here, we investigate if geographic and climate variation explains either genetic or phenotypic variation, or both, in the range of the Blue-crowned Manakin, a polychromatic bird species broadly distributed in the Neotropics. We tested the hypotheses of Isolation by distance, Isolation by environment, and Isolation by adaptation through an integrative approach using genetic, colorimetric, geographic, and climatic data. Through Multiple Matrix Regression with Randomization and Mantel correlation statistics, we tested whether intraspecific genetic or phenotypic diversity associates with variation in geographic and climatic distances among localities. Genetic distances were explained by geographic, climatic, and least environmental cost distances, conforming to predictions from IBD and IBE hypotheses, whereas coloration did not vary significantly with geographical or climatic distances. Genetic and colorimetric distances were not correlated, and spatial autocorrelation in climatic data was low. Our results indicate a combined effect of genetic drift and ecological forces in the diversification at the regional scale, and that both stochastic and deterministic processes may operate at a local level in the evolution of adult male plumage coloration