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Cenotes (sinkholes), formed by the dissolution of the carbonate rock, are the most common waterbodies on the Yucatan Peninsula. Despite their unique features and great amount in the region, our knowledge on the biota of cenotes remains fragmentary. Within the present study we analysed chironomid remains from surface sediment of ten cenotes situated in SE Mexico. In total, 20 taxa of 17 genera were recorded, and the total diversity was estimated to ~30 taxa. The most common taxa were Polypedilum (Tripodura) sp., Tanytarsus ortoni-type, Fittkauimyia sp., Labrundinia sp. and Endotribelos sp. There was a great variability in head capsule abundance among cenotes, ranging from 1 to 64 individuals per site with significantly higher number of remains recorded in open cenotes compared to the closed, cavern types. The results indicate that beside ecological features, such as low trophy, oxygen depletion, simplified habitat structure and fish predation, there are also taphonomical processes connected to the specific nature of cenotes that can hinder the accumulation of biological remains in the sediment. We conclude that due to poor sedimentation and preservation of remains, cenotes have limited potential for palaeolimnological studies.