A method based on high performance liquid chromatography-mass spectrometry(HPLC-MS) for analy-sis of the main molecular species of phosphatidylcholine(PC) and phosphatidylethanolamine(PE) in duck muscle was established.Intramuscular phospholipids was fractionated using solid phase extraction column(NH2),then PC and PE was separated by high performance liquid chromatography(HPLC) with a normal phase semi-preparative silica gel column(Waters μPorosil 300 mm × 7.8 mmi.d,10 μm).The compositions of their molecular species were identi-fied using reverse phase liquid chromatography-electrospray ionization mass spectrometry.The results shows that there were five main molecular species in PC from duck muscle: C20:4 /C16:0 PC,C18:1 /C16:0 PC,C18:2 /C18:0 PC,C18:2 /C16:0 PC and C18:1 /C18:0 PC.There were also five main molecular species in PE from duck muscle: C14:0 /C22:4 PE,C18:0 / C20:4 PE,C18:0 /C18:2 PE,C14:1 /C24:2 PE and C18:1 /C18:2 PE.The main fatty acids composition of PC and PE calculated based on the molecular species results agreed with the results obtained by gas chromatography-mass spectrometry(GC-MS) on the whole.