This study presents the first systematic documentation of thecamoebians and foraminifera in anchialine cenotes (sinkholes) from Quintana Roo, Mexico. Thirty-three surface sediment samples (upper 5 cm) were collected from cenotes Carwash (1.5 psu), Maya Blue (2.9 psu) and El Eden (>3.3 psu). Q-mode cluster analysis of the faunal distributions isolated four low-diversity (Shannon diversity index 1.0–1.5) and salinity-controlled assemblages. Assemblage 1 (1.5 psu) is dominated by the thecamoebians Centropyxis aculeata “aculeata” (53%) and Arcella vulgaris (21%). Assemblage 2 (2.9 ± 0.2 psu) is dominated by Centropyxis aculeata “discoides” (41%) and Centropyxis aculeata “aculeata” (27%). Dwarfed (~50 μm) Centropyxis constricta “aerophila” (20%) with an autogenous test and Jadammina macrescens (29%) dominate Assemblage 3 (3.4 ± 0.2 psu). Finally, Ammonia tepida (51%), Tritaxis sp. (29%) and Elphidium sp. (11%) dominate Assemblage 4 (3.7 ± 0.4 psu). Thecamoebian and foraminiferal populations in the subtropical cenotes are distributed according to salinity variations as found in other temperate paralic systems. The centropyxid taxa trended towards ecophenotypes without spines with increasing salinity, and dwarfed and autogenous-shelled Centropyxis constricta “aerophila” were determined as the most euryhaline thecamoebian, persisting at the ecological boundary of the group (~3.3 psu). Importantly, the transition from a thecamoebian-dominated assemblage to a foraminiferan-dominated assemblage occurs at a salinity of approximately 3.5 psu.