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Most paleolimnological studies based on cladoceran subfossils are from the northern latitudes while the southern hemisphere and in particular, the equatorial area is a less explored area. Cladocera (Crustacea: Branchiopoda) biodiversity was examined in sediment assemblages in La Tembladera Lake, on the southern coast of Ecuador. We found remains from 14 Cladocera taxa belonging to three families: Sididae, Daphnidae and Chydoridae. Then, cladoceran remains together with plant macrofossils and biogeochemistry data were used to infer changes during the last century in this ecosystem. Early in the sediment sequence (ca. AD 1750-1963), we identified changes in cladoceran sub-fossils related to shifts in the hydrologic regime associated with flood frequency (El Niño or minor scale damming). Chydorus and Euricercus seems to skip the dilution effect experienced by other cladocerans during flood events. In ca. AD 1963, the construction of a sluice gate to store water in the northern margin of the lake led to an increase in the littoral area (Pistia stratiotes, Eichhornia crassipes, Typha latifolia, Cyperaceae). This favored the littoral cladoceran Kurzia. Recently, a shift in top predators (fishes and invertebrates) was recorded in the sediment record as an increase in big cladoceran taxa (Ceriophania and Sarsilatona) and in the number of total number of cladocera ephippia. We succeeded to make inferences based on cladoceran remains but we found some problems derived from 1) identifications at genus level, instead of at species level, 2) the general ecological information for some genus and especially, 3) the presence of multiple stressors in recent times, which make much more complex the interpretations. Future studies on cladoceran taxonomy and autoecology should be carry out in equatorial latitudes to refine palaeoecological interpretations based on cladocerans subfossils.