The species-level taxonomy of fat snooks (Centropomus parallelus and Centropomus mexicanus), which are distributed in coastal waters from Florida to Brazil and parts of the Gulf of Mexico, was explored with mitochondrial DNA 16S rRNA and cytochrome c oxidase subunit 1 sequencing and multilocus microsatellite DNA genotyping. The existence of a novel lineage first observed from Puerto Rico (Lineage 3) was confirmed in the presence of specimens of C. parallelus from Florida (Lineage 1), and C. mexicanus from Texas (Lineage 2). The novel lineage was found to be in the same phylogenetic clade as specimens from Brazil, consistent with distribution along the Caribbean coast as far as South America. Lineages 1 and 2 are spatially isolated, with no fat snook reported from Pensacola, Florida to Freeport, Texas. The transition zone between lineages 2 and 3 may occur in the area between the Yucatán Peninsula and western Panama. Sampling from this region is necessary to identify the breakpoint and potential for hybridization. Analysis of sequence data within a maximum likelihood framework revealed that all three lineages form a monophyletic clade within Centropomus, with Lineage 3 as ancestral to the other two lineages. Lineage 3 may have originated in South America and expanded to seed the other two lineages. This expansion is estimated to have occurred 0.9–2.5 million years ago. Lineage 3 individuals occasionally migrate to the Atlantic coast of Florida from the distal area of their distribution range and hybridize with local specimens of Lineage 1, suggesting some overlap in the distribution of these two lineages. Overall, these data suggest a complex underlying phylogenetic history of fat snooks in the western Atlantic, with the potential for future taxonomic revision.