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We documented the nearshore ray-finned fishes in Puerto Morelos Reef National Park (PMRNP) by sampling 57 localities, including rocky intertidal pools, sandy bottoms, Thalassia beds, coral reefs, artificial reefs, karstic-slab bottoms, demersal-pelagic areas, and sessile-Sargassum patches. We recorded seven species new to Caribbean Mexican waters and one hundred and six species new to the PMRNP, most of which are small cryptobenthic reef fish. The resultant checklist includes 349 species, and specimens of 285 of which (81.7%) have been deposited in an ichthyological museum collection. These include both voucher organisms and with tissue samples for genetic analysis. A comparison with inventories at other localities of the Greater Caribbean indicates that more targeted sampling for cryptobenthic and deep-reef fishes is needed to provide a complete inventory. We also comment on the local use of some species as fishery resources.