The possible origin of the Scarlet ibis population of Cubatão in southern Brazil, and its levels of genetic diversity and differentiation in relation to populations from the country’s northern coast were investigated through the sequences of 980 base pairs of β-fibrinogen intron 7 from a sample of 37 specimens. A total of 19 haplotypes were recorded in the three populations. Despite observed discrepancies in the levels of genetic diversity (π = 0.0017–0.0033; h = 0.60–0.95), AMOVA, K*st and Fst values all indicated that genetic differentiation among the populations was relatively low. This suggests that the Cubatão population was isolated recently from the panmictic population that was once distributed all along the Brazilian coast, although it does not totally refute its possible derivation from a specific population on the north coast. Given our results, genetic management should focus on the minimization of inbreeding, especially in the smaller populations, such as Cubatão. However, a more definitive study, including markers with higher evolutionary rates (e.g. microsatellites) and a much larger sample, would be required before any such actions can be taken.