Rhizopus rot, caused by Rhizopus stolonifer, is a major postharvest disease of stone fruits. The disease is related to the occurrence of mechanical and physical damage; however, observations at a Brazilian wholesale market suggest that direct penetration can occur. Therefore, the penetration mechanisms of R. stolonifer in stone fruits were evaluated. To identify the production of enzymes that help with direct penetration by the pathogen, esterase activity, both in mycelial discs and in spore suspensions of the fungus in water and in modified Van Etten nutrient solution, was measured. Assays were also conducted to evaluate the growth of R. stolonifer on glucose or cutin as a sole carbon source. The pathogen grew on both media, and higher esterase activity was observed in the cutin medium. Wounded and unwounded peaches and nectarines were inoculated with R. stolonifer spore suspensions in water or in modified Van Etten nutrient solution. Wounded fruit inoculated with either of the R. stolonifer spore suspensions developed rhizopus rot, whereas unwounded fruit developed the rot only in the presence of spores in the modified Van Etten nutrient solution. Scanning electron and light microscopic examination showed the fungus can directly penetrate the nectarine cuticle. Diisopropyl fluorophosphate, a serine hydrolase inhibitor, prevented rot development in peaches. The results provide valuable evidence for the ability of R. stolonifer to directly penetrate unwounded stone fruits, probably due to the production of esterase enzymes.