An endophytic oleaginous fungus Salicorn 5 has been isolated from Salicornia bigelovii Torr. and characterized as Cunninghamella sp. based on its morphological characteristics and ITS1-5.8S-ITS2 gene sequence analysis. The individual lipid compositions produced by Salicorn 5 were isolated and determined to be (1) oleic acid, (2) linoleic acid, (3) γ-linolenic acid (GLA), (4) 2,3-dihydroxypropyl oleate, (5) 2,3-dihydroxypropyl stearate, (6) 1,3-diolein, (7) 1,2-diolein, (8) 1,3-2-oleyl,2-stearoyl triacylglycerol, (9) ergosterol peroxide, (10) stigmasta-7,22-diene-3β,5α,6α-triol, (11) stigmasterol, and (12) ergosterol. The chemical structures of these compounds were determined by a combination of electrospray ionization mass spectrometry (ESI–MS) and nuclear magnetic resonance (NMR) analysis, as well as a comparison with data from the literature. Analysis of the fatty acids showed that they were composed predominantly of polyunsaturated fatty acids (PUFAs), including oleic acid (35.57 %), linoleic acid (21.58 %), palmitoleic acid (16.31 %), and linolenic acid (13.28 %), whereas stearic acid, palmitoleic acid, myristic acid, arachidic acid, and eicosenoic acid were found in lower amounts. These results could therefore provide a useful platform for fully exploring the potential application of oleaginous fungus Salicorn 5, and optimizing of the fermentation conditions for producing the PUFAs and high-value GLA, as well as providing further insight into the relationship between endophytes and their hosts.