Knowledge of the breed-specific and tissue-specific lipid molecular composition is helpful to understanding the complicated mechanisms of lipid deposition. In this study, a liquid chromatography (LC)-mass spectrometry (MS)-based lipidomics approach was used to discriminate chicken meat and abdominal fat from different sources. OxPC (16:0-20:4+1O(1Cyc)) and PC (18:2/20:5) were determined as the discriminatory markers for the meat of Guangyuan grey chicken, Jiuyuan black chicken and Tibetan chicken. A total of 209 lipid molecules were commonly determined as marker candidates for abdominal fat and intramuscular fat authentication, among which glycerophospholipids was the dominant class. Acylcarnitine (Acar), ceramides (Cer), cardiolipin (CL), fatty acid (FA), glucosylceramides (GlcCer), phosphatidic acids (PA), phosphatidylcholines (PC), phosphatidylethanolamines (PE), phosphatidylglycerols (PG), phosphatidylinositols (PI), phosphatidylserines (PS), sphingomyelines (SM), triacylglycerols (TAG) contributed significantly to these differences. The higher abundance of sphingolipid and PUFA-enriched glycerophospholipids in the intramuscular fat elucidated its beneficial roles in imparting a characteristic flavor and nutritional value to meat. Future investigation is required to combine these lipid metabolites with underlying molecular mechanisms to regulate and optimize body fat distribution in chickens. ● Breed-specific and tissue-specific lipid molecular composition was characterized ● Glycerophospholipids were the most dominant class in both tissues ● 209 lipid molecules were determined as discriminatory markers for abdominal fat and intramuscular fat authentication ● The chicken meat had higher sphingolipid and PUFA-enriched glycerophospholipids [ABSTRACT FROM AUTHOR]