Abstract Non-polar and polar lipids were isolated from Methanopyrus kandleri. Non-polar lipids accounted for 50% w/w of total lipids, with a high proportion of 2,3-di-O-geranylgeranyl-sn-glycerol, 2,3-di-O-phytanyl-sn-glycerol and geranylgeraniol. The core lipids prepared by mild acid methanolysis consisted exclusively of 2,3-di-O-phytanyl-sn-glycerol. Two-dimensional TLC showed mostly glycolipids, and minor amounts of aminophospholipids, phosphoglycolipids and phospholipids. The purification yielded three diglycosyl-lipids (50% of total polar lipids), one triglycosyl-lipid (5%) and six glycosyl-lipids with five glycosyl-groups (36%), which consisted of glucose, galactose and mannose. The lipid analysis supports the unique position of Methanopyrus kandleri within the 16S rRNA-based phylogenetic tree.