This first analysis of the marine fish fossil record in the Caribbean region during the Neogene is based on comprehensive new faunal compilation lists at the generic level from basins of nine Central and South American countries during Miocene and Pliocene times. Joint ordination and classification techniques were used to analyze data comprising 236 genera and 346 species. Principal Component Analyses were used to calculate covariance and variance between localities. We identified four subprovinces, representing four different patterns. The subprovince of Venezuela shows distinct and unique features since the Neogene in the diversity of ecosystems represented. The Antillean subprovince has a western orientation and is composed of Jamaica, the Dominican Republic, and the Trinidad islands. The third subprovince combines Panama and Ecuador. It reflects the Pacific faunal influence into the proto-Caribbean and a characteristic benthopelagic fauna. The fourth subprovince is Costarican. Its nektonic fish fauna reflects the overprinting impact over the proto-Caribbean fish fauna mostly due to local paleoenvironmental changes (neritic, estuarine and deep water assemblages), whereby the overall composition of genera is largely not affected (except few lamnids, such as the giant-toothed white sharks and the wide-toothed mako shark). The results of the analyses are concordant with previous ones based on invertebrates and identified regions in need of study (e.g., Colombia, Nicaragua, Honduras, and Brazil).