The fatty acid compositions of six Arctic and fourteen Antarctic macroalgae species (Rhodophyta, Phaeophyta and Chlorophyta) from Kongsfjord (West-Spitsbergen) and King George Island (Antarctic Peninsula) were investigated. The macroalgae were cultivated in nutrient-enriched seawater at low temperatures (0-5°C) and light conditions similar to natural irradiance. The most abundant fatty acids in the Arctic and Antarctic Rhodophyta were generally 20:5(n-3) and 16:0. The Arctic Palmaria palmata and the Antarctic Audouinella purpurea were characterised by very high proportions of 20:5(n-3) (67.3 and 60.3%, respectively). Other important fatty acids were 16:1(n-7) and 20:4(n-6). Two species were dominated by 20:4(n-6) (Phycodrys rubens 35.3% and Delesseria lancifolia 31.1%). In Ptilota gunneri and Rhodymenia subantarctica 16:1(n-7) accounted for 39.9 and 32.7%, respectively. In the Phaeophyta major polyunsaturated fatty acids were 18:4(n-3), 20:5(n-3) and 20:4(n-6) followed by 18:3(n-3) and 18:2(n-6). The principal saturated fatty acid was 16:0. A high percentage of the uncommon monounsaturated fatty acid 16:1(n-5) (11.1%) was found in Desmarestia mülleri sporophytes. Their gametophytes exhibited only traces of this component, but instead had double the amount of 18:2(n-6) and 18:3(n-3). The Arctic Chlorophyta Prasiola crispa and the Antarctic Lambia antarctica had fatty acid compositions dominated by the polyunsaturated fatty acids, 18:3(n-3) and 18:2(n-6). In L. antarctica 18:1(n-7) was present in higher levels than 18:2(n-6). The clear differences in fatty acid compositions of the three taxa are probably due to their different evolutionary position. The high proportions of 20:5(n-3) in Rhodophyta reflect a marine-like character and hence the phylogenetically oldest lineage. Chlorophyta is the most modern group which is supported by primarily C18 unsaturated fatty acids typical for vegetative tissue of higher plants. The fatty acid compositions of Phaeophyta support their intermediate position. The clear differences between the macroalgae taxa, and also variations between species make fatty acids a potential tracer for studies of food web interactions.