Diatoms were analysed from a 30-cm long sediment core obtained from remote subarctic Lake Saanaärvi (69°03′N, 20°52′E) in order to trace possible changes in the lake. Diatom assemblages were relatively constant throughout the core, except in the top 4–5 cm (≈ 1850 A.D.) where relative frequencies of Aulacoseira italica subsp. subarctica, A. lirata var. biseriata, Cyclotella comensis and C. glomerata increased markedly. No significant trends were observed in the weighted averaging (WA) reconstructed pH values. Several hypotheses, including (i) airborne pollution, (ii) climatic change, and (iii) catchment disturbances have been put forth to explain the recent changes in diatom assemblages. The diatom change coincides with a marked increase in mean annual temperature that has been documented in the area since the termination of the Little Ice Age. Our evidence favours climate change as the main causative mechanism for the observed diatom compositional changes, although other explanations cannot be ruled out.