Background: Staphylococcus epidermidis causes prosthetic valve endocarditis, urinary tract infection, and implant-related infections. These are difficult to treat often due to drug resistance, particularly because S. epidermidis biofilms are inherently resistant to most antibiotics. Salvia miltiorrhiza is a kind of sichuan-specific medicinal herb, and has effective ingredients, such as cryptotanshinone. Cryptotanshinone was demonstrated to have anti-microbial properties and no resistance. Objectives: The current study investigated the effects of cryptotanshinone on S. epidermidis biofilm formation, and found new agents controlling S. epidermidis biofilm formation and resistance caused by biofilm. Methods: The effects were further analyzed by crystal violet assay (CV), 2, 3-bis [2-methoxy-4-nitro-5-sulfophenyl]-2H-tetrazolium-5-carboxanilide inner salt assay (XTT), and scanning electron microscopy (SEM). The qRT-PCR assay was used to determine the expressions of biofilm key genes, including icaA, atlE, aap and luxS. Results: The amount treated by cryptotanshinone was reduced compared with the non-treating group, so did the metabolic activity inside the biofilm. Even the micro-structure was destroyed with cryptotanshinone. The expressions of biofilm key genes, including icaA, atlE, aap, and luxS, were down-regulated by cryptotanshinone. Conclusions: There is new insight that cryptotanshinone could inhibit immature biofilms and the down-regulations of icaA, atlE, aap, and luxS might explain this inhibitory effect.