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Thermokarst ponds are widespread in arctic and subarctic regions, but little is known about their temporal evolution prior to human observations. This paper presents a pioneer biostratigraphic study conducted at a subarctic site with limnologically contrasted ponds located on the eastern shore of Hudson Bay, Canada. Fossil diatom and visible near infrared (VNIR) derivative spectral analyses were performed on short sediment cores, confirming the occurrence of three distinct stratigraphic facies as already inferred from an anterior sedimentological study: a lacustrine upper facies (UF) and a marine lower facies (LF), separated by an organic-rich/peat transitional zone (TZ). Diatoms were almost absent from LF, but increased significantly in both TZ and UF. Identified diatom taxa were mainly benthic species (e.g. genera Fragilaria, Pinnularia), and their down-core distribution appeared to be related to dissolved organic carbon (DOC) and possibly pH conditions. Diatom-inferred DOC showed a decreasing trend towards the surface (potentially associated with an increase in pH), inverse to the general trend in this region, suggesting the action of other mechanisms on DOC, such as exhaustion of external inputs from limited catchments and the role of discontinuous peat layers (former surfaces of permafrost mounds) during the initial stages of pond formation. These bryophilous substrates in aerophilic habitats probably controlled diatom community composition. The combination of diatom and VNIR data revealed similar trends between (i) opal (amorphous silica) and diatom abundances; (ii) eukaryotic/prokaryotic algae ratio and anoxia or hypoxia in bottom waters; and (iii) limonite (iron oxide) and redox conditions in surface sediments. These findings indicate that diatom community changes and pond limnological evolution in the recent past were controlled mainly by autogenic processes (e.g. local vegetation/soil development, peat accumulation and erosion), rather than by allogenic forcing mechanisms (e.g. precipitation and temperature, geochemical leaching of the surrounding glaciomarine sediments).