Thermokarst lake deposits are useful archives of climatic and environmental changes in the past, and can contain palaeo-bioindicators such as pollen, plant macro-fossils, diatoms, chironomids and also ostracods. Nevertheless, such studies from permafrost regions including thermokarst lake deposits are still rare. We studied late Holocene ostracods from an excavation of deposits of the Aalas Myuryu in Central Yakutia. In order to apply modern data to fossil records, we also studied the present-day relationships between the environmental setting and the geochemical properties of ostracods in six thermokarst lakes of the same region. The fossil ostracod record reflects lake-level fluctuations in both species composition and stable isotope data (δ18O, δ13C). The modern ostracod communities of thermokarst lakes in Central Yakutia are broadly similar to those of Holocene age. Geochemical stable isotopes studies in both modern host water and ostracod calcite are a prerequisite for further interpretation of the fossil records.