Ganoderma lucidum is a mushroom with a long history of medical applications. Research has demonstrated chemotherapeutic effects of G. lucidum in tissue culture, and bioactive fractions of the mushroom have been shown to contain high levels of triterpenoids and polysaccharides. In this study, we developed a new method for the detection of ganoderic acids and other triterpenes in Ganoderma mushroom extracts based on a post-biosynthetic stable isotope encoding technique. Overall, 57 doublets were identified as potential ganoderic acids and 11 of those matched with the database. Ganoderic acid A, F and H were confirmed by standards and their absolute concentrations were measured in GLT (GA A: 3.88 mg/g; GA F: 0.95 mg/g and GA H: 1.74 mg/g) and ReishiMax (GA A: 2.32 mg/g; GA F: 0.43 mg/g and GA H: 0.85 mg/g) extracts. The method was also used for the evaluation of bioavailability of triterpenes after an oral application and demonstrated the presence of G. lucidum triterpenes in plasma.