Abstract Tetraodontidae is the most speciose family of Tetraodontiformes and is represented by fish popularly known as pufferfishes. They are characterized by modified jaws with four dental plates and the ability to inflate their bodies. Tetraodontids are distributed throughout the world and have a wide range of habitat use. One of its genera, Sphoeroides, shows a biogeographical pattern, with 19 of its 21 species restricted to coastal regions of the Americas. Although represented in large-scale phylogenies, the evolutionary history and biogeography of the genus have not been explored in detail. The present study aims to understand the historical and biogeographic processes that shaped the evolutionary history of Sphoeroides. Including samples from all biogeographic regions of its occurrence, we reconstruct a phylogenetic/biogeographic history hypothesis for the genus. Our results show that Sphoeroides is a paraphyletic group comprising Colomesus; indicate a central role of the biogeographic barriers of the Atlantic Ocean in the diversification of the genus; and identified a cryptic species in Brazilian waters, formally known as S. spengleri, described here through integrative taxonomy. We also propose nomenclatural changes given the position of Colomesus deeply nested within Sphoeroides.