The Scarlet Ibis (Eudocimus ruber) and White Ibis (Eudocimus albus) are often classified as separate species, but differing scientific opinions exist regarding the taxonomic status of these birds, as they exhibit similar behavior and hybridize in nature. The present study provides genetic data to help clarify this taxonomic issue. DNA was extracted from 10 individuals of each taxon from the states of Florida, USA (White Ibis) and Amapá, Brazil (Scarlet Ibis). The sequences of three mitochondrial and four nuclear markers were obtained from all individuals. The Scarlet Ibis and White Ibis did not share any haplotypes in mitochondrial genes nor in one nuclear marker. Species delimitation using Bayesian analysis, the Knowles-Carstens method and the genealogical sorting index demonstrated the Scarlet Ibis and White Ibis to be two different lineages and revealed a strong signal of speciation despite the polyphyly found in three of the four nuclear markers.