The Wood Stork (Mycteria americana) is a wading bird inhabiting subtropical and tropical regions of the American continent. This species is considered endangered in the United States. We compared variability and genetic structuring of nine Brazilian Pantanal subpopulations with an North American population using eight allozyme loci data (MPI, ICD, NSP, EST-D, LDH, PGM, 6PGD, and PEP-A) and four microsatellite loci data (WS1, WS2, WS4, and WS6). Average expected heterozygosity of Pantanal population was similar (0.198 ± 0.065) to that expected for the North American population (0.231 ± 0.066). No significant genetic differentiation was found among Pantanal subpopulations (F_st = 0.012) and low differentiation was detected between Pantanal and North American populations (F_st = 0.023). Lack of differentiation among Pantanal subpopulations may have been due to high gene flow level among birds of neighbor breeding colonies and low natal philopatry. We propose that low differentiation between North and South American populations has arisen either because these populations occupied neighboring regions during late glaciation or because there is a continuous gene flow between them, via Central American or northern South American populations.