Structural identities of the major phospholipid (PL-2), minor phospholipid (PL-1) and trace phospholipid (PL-0) from representative strains of the genera Thermus and Meiothermus were established. Phospholipids were quantified using phosphorus-31 nuclear magnetic resonance ((31)P-NMR). The structures of the major phospholipid (PL-2) from Thermus filiformis MOK14.7 and Meiothermus ruber WRG6.9 were identified as 2'-O-(1,2-diacyl-sn-glycero-3-phospho)-3'-O-(α-N-acetylglucosaminyl)-N-glyceroyl alkylamine (GlcNAc-PGAA) and 2'-O-(2-acylalkyldiol-1-O-phospho)-3'-O-(α-N-acetylglucosaminyl)-N-glyceroyl alkylamine (GlcNAc-diolPGAA). Interestingly, M. ruber contained only a diacyl form of GlcNAc-PGAA (87 %), while T. filiformis contained both GlcNAc-PGAA (59 %) and GlcNAc-diolPGAA (18 %). The structures of the minor phospholipid (PL-1) were established as 2'-O-(1,2-diacyl-sn-glycero-3-phospho)-3'-O-(α-glucosaminyl)-N-glyceroyl alkylamine (GlcN-PGAA, 13 %) in T. filiformis and 2'-O-(1,2-diacyl-sn-glycero-3-phospho)-3'-O-(α-galactosaminyl)-N-glyceroyl alkylamine (GalN-PGAA, 19 %) in M. ruber. This is the first reliable discovery of phosphatidylglyceroylalkylamines modified by glucosamine or galactosamine with a free amino group. No signs of diol-based phosphatidylglyceroylalkylamines were found in PL-1 phospholipids. Similar to PL-2, trace phospholipid (PL-0) from T. filiformis contained both unsubstituted diol-based phosphatidylglyceroylalkylamine (diolPGAA) and PGAA, while M. ruber contained only free PGAA. Unlike analysis using TLC, the diol form of phosphatidylglyceroylalkylamines is clearly resolved from the diacyl form via (31)P-NMR.