The family Rallidae is a distinct, species-rich group of birds, many of which are exceptional at long-distance colonization. Six of the ten species in the genus Rallus are distributed in the Americas. Among these, R. longirostris and R. elegans have an interwoven taxonomic history that reflects their weak phenotypic differentiation, the multiplicity of allopatric, morphologically distinct populations, a long zone of secondary contact in the eastern U.S. along which hybridization occurs, and apparent ecological “replacement” of each other in marshes of varying salinity. We used mitochondrial and nuclear gene sequences, the latter generated from next-generation sequencing, to infer phylogenetic relationships in the complex from a sample of 70 individuals collected throughout their distribution. Average levels of mitochondrial and nuclear divergence were relatively low (<2%) both within and between the species. The complex is composed of three distinct biogeographic groups: (1) eastern North America and the Caribbean, (2) South America, and (3) western North America, including Mexico. Our results indicate that R. elegans as currently recognized is paraphyletic, with birds of the highlands of Mexico sister to R. longirostris of California. Rallus elegans of eastern North America and Cuba is sister to R. longirostris from eastern North America and the Caribbean. This paraphyly, along with the reproductive isolation of the ecologically divergent R. elegans and R. longirostris in the eastern United States, supports splitting the complex into five morphologically and genetically distinct species.