The formation of the Isthmus of Panama during the Late Pliocene was a pivotal event in shaping continental biodiversity in the Americas. However, our understanding of the resulting Great American Biotic Interchange (GABI) relies heavily on fossil assemblages from Central America, which remain poorly constrained in terms of composition, depositional context and geological age. This study investigates the host strata, taphonomy and paleoecological significance of vertebrate faunas from Pedro Creek near Santa Rita de Limoncito, southeastern Costa Rica, based on ongoing excavations, high-resolution sedimentological profiling, taphonomic assessment, and geochronological analyses. Most vertebrate remains in this locality occur in two thick, massive intraclast conglomerates interbedded with sandstones and mudrocks of the marginal-marine San Gerardo unit (Upper Miocene). The taphocoenoses are poorly sorted, comprising isolated, disarticulated or fragmentary, relatively unweathered fossils. Based on the Voorhies classification for alluvial vertebrate assemblages, most fossils correspond to Group 1 – bones that are most easily transported. A comparative sample of reworked fossils from the streambed reflects 95% Group 1 and 5% Group 2, indicating progressive hydraulic winnowing. The assemblages include elasmobranch teeth, crocodyliforms and testudines remains (jaw fragments and dermal plates), and a mixture of North American (camels, horses including Equus, gomphotherids) and South American taxa (giant armadillos like Scirrotherium, ground sloths). These findings indicate that the terrestrial vertebrate fossils from Santa Rita de Limoncito are allochthonous elements in fan-delta deposits and provide evidence of faunal exchange across Central America prior to full emergence of the isthmian land bridge.