This paper addresses a comprehensive and comparative study of six phytochemical extraction methods for triterpenes from the fruiting body of Ganoderma spp. Quantitative analysis of extracts was performed by HPLC with photodiode array detection. In general, pressurized liquid extraction and microwave-assisted extraction under optimized conditions produce better yields, and the former also significantly reduces the total time of extraction and manipulation of a sample, as well as the amount of solvent used in comparison with conventional soxhlet, reflux, ultrasonic, and methanol–CO2 supercritical fluid extractions. Based on the improved extraction protocol, the fingerprinting profiles for two species of Lingzhi were established using the consistent chromatographic features of 12 authentic samples. Eleven common peaks of ganoderic/ganoderenic acids were identified using LC-ESI-MS-MS. These specific triterpene groups were adopted as chemical markers for Lingzhi. Using chemometric analysis, the developed fingerprinting was successfully applied to differentiate between the two species under the Ganoderma genus and is applicable as a method for quality evaluation of this valuable medicinal fungus and its related proprietary products. Copyright © 2008 John Wiley & Sons, Ltd.