The fatty acid (FA) composition of zooplankton has taxon-specific characteristics but may also be influenced by various environmental factors. Abiotic properties of lakes (location, morphometry, water chemistry and temperature) shape the phytoplankton community structure. We studied how this may be manifested in the FA composition of the common freshwater calanoid copepod Eudiaptomus spp. The proportions of saturated and polyunsaturated FA in Eudiaptomus, sampled from 25 lakes in boreal and subarctic regions, showed large variation (ca. 20-60 and 30-70%, respectively), while the proportion of monounsaturated FA was less variable (5-15%). The FA composition of Eudiaptomus differed significantly between subarctic and boreal lakes. Eudiaptomus from subarctic lakes had a higher proportion of 22:6ω3 and lower proportions of 18:2ω6, 18:3ω3 and 20:5ω3 than Eudiaptomus from boreal lakes. In the boreal lakes, the ω3:ω6 ratio in Eudiaptomus increased with increasing nutrients, chl a and dissolved organic carbon, presumably due to parallel changes in phytoplankton community composition, but only in the large and clearwater lakes, and not in the small and humic ones. Copepods are seasonally important prey for planktivorous fish, and the observed among-lake differences in the proportions of essential FA may influence fish growth and reproduction.