Free and esterified ergosterols are detected almost solely in fungi and are often employed as a biomarker of living fungi. In this work, the fatty acid composition and δ13C values of major fatty acids in triglycerides and ergosteryl esters from the fungus Ganoderma lucidum were analyzed by gas chromatography–mass spectrometer and gas chromatography–isotopic ratio mass spectrometer, respectively. The results showed that the fatty acid profiles varied in triglycerides and ergosteryl esters. The percentage of saturated fatty acids in ergosteryl esters was remarkably higher than that in triglycerides, where C18:1Δ9c was the predominant fatty acid and constituted 61.26 % of the total fatty acids. In contrast, C16:0 was the predominant fatty acid and constituted 71.88 % of the total fatty acids in ergosteryl esters. The study suggests that, after fungal death, free ergosterols in the cell membrane of the dead fungus were esterified with preferentially saturated fatty acids, mainly C16:0, from triglycerides and then stored in lipid particles for a longer period while free ergosterol markedly decreased. The δ13C values of C16:0, C18:0, C18:1 and C18:2 in ergosteryl esters exhibit a pronounced depletion in 13C compared with that in triglycerides within the range of −1.3 to −0.9 ‰, supporting the above inference. It is again suggested that free ergosterol in the cell membrane should be used as an indicator of living fungi, and ergosteryl esters in the lipid particles should not be included in the measurement of living fungal biomass.