We tested the response of lacustrine testate amoebae (thecamoebians) to climate and environmental changes for the Lateglacial-Holocene transition. The palaeoenvironmental history of the study site (Lake Lautrey, Jura Mountains, eastern France) was previously established based on high-resolution multi-proxy studies of the same core. The present study is characterised by a high taxonomic resolution (54 taxa), inclusion of small species (clown to 25 mu m) and high total counts (>500 individuals per sample on average). Changes in the composition of testate amoeba assemblages (dominant species and assemblage structure), as well as in the accumulation rate (tests cm(-2) a(-1)), corresponded to major climatic phases (i.e. Oldest Dryas, Bolling-Allerod Interstadial, Younger Dryas, Preboreal) as well as changes in organic matter inputs. Furthermore, decreases in the accumulation rate characterised minor short-lived cooling events, such as Older Dryas event or Gerzensee oscillation. However, the Preboreal oscillation, which was well registered by other proxies at Lake Lautrey, could not be recognised in the testate amoeba record. This work demonstrates that lacustrine testate amoebae can be used for palaeoclimatic and palaeoecological reconstructions. Nevertheless, a better understanding of the relation between climate, organic matter and lacustrine testate amoebae requires further high-resolution studies based on multi-proxy approaches and the development of appropriate modern analogues. Copyright (C) 2010 John Wiley & Sons, Ltd.