The goal of this study is to evaluate for the first time the composition of triacylglycerols (TAG) using ESI-TOF-MS and phospholipids species using HPLC-ESI-TOF-MS of two Capparis spinosa seed oil populations. Results show that LOO, LOP, LLO, OOO, PLL and POO were the major molecular species of triacylglycerol detected in caper seeds; where L represents linoleic acid; O, oleic acid; and P, palmitic acid. The TAG composition was significantly different among the two C. spinosa populations. In Ghar el Melh population, LOO (15.7%) was detected as the dominant TAG molecular species, followed by LOP (13.2%), LLO (12.0%) and OOO (11.4%); while, the dominant fraction was LLO (14.2%) followed by LOO (14.1%), LOP (11.5%) and PLL (10.5%) in Chouigui samples. The major component in the phospholipids fraction was phosphatidylinositol (ca. 54-91%), followed by phosphatidylglycerol, phosphatidylethanolamine and phosphatidic acid. A variety of molecular species within each class were identified. The major component in all phospholipids species contains a C-18:1 lipid chain. C16:0/C18:2-PI (ca. 28-31%) was the most abundant PI. PG species were mainly C18:2/ C18:1-PG (25-32%). The major PE was C18:1/C18:1-PE (44-75%). The major PA species was C18:1/C18:1-PA (22-24%).