Genotype and phenotype in mobile organisms can be de ned by various factors such as environmental, biological and geographical. Brown noddies Anous stolidus are pan-tropical seabirds breeding at different times, with migratory and resident populations in six islands throughout 20° of latitude in the Southwestern Atlantic Ocean. If environmental heterogeneity plays a key role in their population biology, we would expect signi cant genetic structure and/or phenotypic variation among colonies. However, absence of genetic structure between phenotypically different populations could play a scenario of ecological plasticity. To test these hypotheses, we used a model-based integrative approach combining genetic (mtDNA and ultraconserved elements) and morphological data of the brown noddy (n = 122) along with environmental variables and isotopic niches. We uncovered low levels of genetic structure, with 16 haplotypes for mtDNA and a signal of an ancient population expansion. Ultraconserved elements indicated that all colonies belong to the same genetic population (K = 1) and revealed substantial endogamy. However, phenotype differed both by biometric measures and isotopic niches between most pairs of populations. Although individuals from the northernmost colony are larger than the others, they are genetically similar, indicating a wide reaction norm for this species. Our results indicate the Southwestern Atlantic populations of the brown noddy are panmictic, but ecologically and morphologically diverse.