High-resolution palaeolimnological data from a number of remote and nonpolluted lakes in Finnish Lapland reveal a distinct change in diatom assemblages. This parallels the post-19th century Arctic warming detected by examination of long-term instrumental series, historical records of ice cover and tree-ring measurements. The change was predominantly from benthos to plankton and affected the overall diatom species richness. A particularly strong relationship was found between spring temperatures and compositional structure of diatoms. The change is irrespective of the lake type and catchment characteristics, and is reflected by several other biological indicators, such as chrysophytes and zooplankton, suggesting that entire lake ecosystems have been affected. No corresponding change in the diatom-inferred lake-water pH was observed; hence, atmospheric fallout of acid substances cannot have been the driving force for the observed biological change. The mechanism behind the diatom response is unclear, but it may be related to decreased ice-cover duration, prolonged growing season and increased thermal stability. We postulate that 19th century Arctic warming, rather than acidic or other anthropogenic deposition, is responsible for the recent ecological changes in these high latitude lakes.