The phylogeny of the genus Dilocarcinus H. Milne Edwards, 1853 and the taxonomic status of Dilocarcinus pagei Stimpson, 1861 lato sensu are investigated using a molecular and morphologic integrative approach. This species is distributed over a large part of Neotropical South America in the Amazon and La Plata (Paraguay–Paraná rivers) hydrographic basins. We evaluated the genetic variability of this species along these river basins to understand the degree of the variability among its representatives, their taxonomic status, and to address the gaps in the north–south distribution that remain despite its wide area of occurrence. The morphological analysis included NanoCT–Scan images, and the molecular analysis was based on mitochondrial markers COI and 16S rRNA and included Maximum Likelihood Trees, Bayesian Inference, Genetics Distance Matrix, and Haplotype Networks. These studies revealed and supported the existence of two cryptic species: a southern one, distributed in the La Plata basin (Paraguay–Paraná basin), that kept the name D. pagei Stimpson, 1861, and a northern one, occurring in the Amazon basin, the name D. cristatus Bott, 1969 was revalidated. We discuss conjecture that Dilocarcinus originated in the western Amazon region between the Middle Eocene and the Lower Miocene (c. 41–19 Ma), most likely in the Oligocene (31 Ma), and later expanded to other regions in southern and eastern South America.