Cladocera (Crustacea: Branchiopoda) quickly respond to changes in environmental conditions and their remains are usually found in large amounts in lacustrine sediments, which make them an important biological proxy in paleolimnological studies. Variations in species composition have been used to infer paleo-climate and paleo-environmental variables including lake depth, eutrophication, and deforestation. However, despite their advantages as bioindicators in the study of past conditions, they are underutilized in paleolimnological research in Central America due to limited knowledge about their diversity and the morphological differences between the subfossil remains of different taxa. In order to address this issue, we described and analyzed cladoceran remains from 56 waterbodies located in Mexico, Guatemala, El Salvador, and Honduras. Here, we provide a description of the remains from 10 different taxa that belong to the Sididae, Bosminidae, Daphniidae, Macrothricidae, and Ilyocryptidae families.