The efficacy of Sporidiobolus pararoseus Y16 in controlling postharvest blue mold caused by Penicillium expansum on apples and the defense response involved were evaluated. The results suggested that the decay incidence of blue mold of apples treated by S. pararoseus Y16 was significantly reduced compared with the control. In vitro testing indicated that germination of spores and germ tube length of P. expansum were markedly inhibited by S. pararoseus Y16. Meanwhile, polyphenol oxidase (PPO), peroxidase (POD), phenylalanine ammonia lyase (PAL), and catalase (CAT) activities and several pathogenesis-related (PR) gene expression levels (including PR3, PR4, PR5, and PR9) were determined. In apples, the activities of PPO, POD, CAT, and PAL were significantly induced by S. pararoseus Y16 treatment compared with the control fruits. The relative expression levels of PR3 and PR4 were significantly induced at 4 and 6 d, while PR5 was significantly induced at 4 and 6 d and PR9 was significantly induced at 4 d. Therefore, the reduction in apple fruit decay by S. pararoseus Y16 treatment could be related to the increased activities of related enzymes and proteins involved in the defense against pathogens, which suggest that S. pararoseus Y16 is a potential antagonistic yeast.