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The examined Ariidae marine catfish from the Neogene of tropical America consisted of isolated skulls, otoliths and bone fragments, some of which were described independently as otolith-based species or skull-based species. We used three-dimensional digital rendering (microCT) of skull and otolith reconstructions to recognize anatomical patterns including skull-otolith morphology, spatial allocations of otoliths in the endocranium for taxonomic identifications. We recognized isolated Proto-Caribbean otoliths of Cathorops sp. from the late early Miocene to early Pliocene formations and isolated otoliths of † Aspistor verumquadriscutis , † Bagre urumacoensis and Notarius sp. from the late Miocene. We explored the endocrania of four fossil Ariidae skulls from the late Oligocene to late early Miocene Proto-Caribbean to determine their internal otolith-cranial morphology, and we identified and described the skulls of † Bagre protocaribbeanus and † Cantarius nolfi and erected the new species of † Bagre castilloensi n. sp. and † Bagre ornatus n. sp. based on the internal otolith-skull association. The first fossil record of Bagre marinus from the early Pliocene Cubagua Formation to the late Pliocene San Gregorio Formation completed the ariid geochronological sequence. We discuss the differential stages of fossil preservation of bioapatite skulls and aragonite otoliths according to the diagenetic processes as well as the paleoenvironmental conditions in the sedimentary basins. Detailed microCT, 3D reconstructions, X-rays, dry prepared skeletons and digital photos of otolith and skull are shown to elucidate the in-skull otoliths species descriptions. • The research provides the first descriptions of Neogene Ariidae catfish in-skull otolith and the erection of new species. • Neogene otoliths and in-skull otolith based species reinforce the paleodiversity of Ariidae. • MicroCT and 3D reconstructions elucidate the fossil in-skull otolith Ariidae species. [ABSTRACT FROM AUTHOR]