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Biodiversity patterns provide insights into the conservation value of ecosystems and also aid in an understanding of some research priorities. This research paper presents an exhaustive inventory of crustaceans and fish species from the Yucatan Peninsula’s epicontinental, underground, and anchialine aquatic systems. Using records spanning from 1936 to 2024, this study analyzed over 2600 entries across 670 aquatic systems, including cenotes, flooded cave lakes, springs, and wetlands. A total of 329 species were recorded, comprising 117 fish and 212 crustacean species. The richness and endemism of these species were assessed through a completeness analysis, utilizing non-parametric models (Chao 2, Jackknife 1, Bootstrap) to estimate potential species richness. Notably, the region exhibits high endemism, especially among crustaceans, with up to 50 species and 2 endemic families being unique to the Yucatan Peninsula. This study underscores the importance of the eastern YP for crustaceans and the central YP for fish, highlighting areas critical for conservation. These findings emphasize the need for further exploration, as the diversity of aquatic species remains incompletely understood. This comprehensive synthesis aims to inform future conservation strategies, environmental management, and regional planning efforts, particularly highlighting the vulnerability of these unique aquatic systems to environmental degradation. Inglés