OBJECTIVE: To determine three hydrophobic components content in Salvia yunnanensis roots collected from different habitats, and compare with Salvia miltiorrhiza Bge. METHODS: The analysis was carried out by RP-HPLC. RESULTS: There was a great different content of three hydrophobic components between Salvia yunnanensis and Salvia militiorrhiza roots. Cryptotanshinone, tanshinone I and tanshinone II A in Salvia miltiorrhiza was 17, 2 and 3 times than those in Salvia yunnanensis. CONCLUSION: The further research must be carried out that if Salvia yunanensis can be as a substitute of Salvia miltiorrhiza or not.