Red pitaya fruit is highly susceptible to fungal infection during postharvest, causing quality deterioration and huge economic losses. This research was intended to isolate, purify and identify the pathogens which cause rotting of red pitaya during storage in Zhejiang Province, screen essential oils for controlling the pathogenic isolates, and test their effectiveness. HS3 and HS6 were identified as pathogens through isolation, purification and pathogenicity tests. These two strains were proved as F. proliferatumandC. fructicola by morphological identification and rDNA-ITS molecular identification. Six essential oils were investigated for their activity to control these pathogens. The result indicated that carvacrol, cinnamon and thyme oil showed complete inhibitory effect on all pathogens at a concentration of 2000μL/L. Then, the inhibitory effects of carcanol, cinnamon and thyme oil on these two pathogens were studied by direct contact in vitro and in vitro fumigation. It was found that carcanol showed higher antifungal activity against F. proliferatum and C. fructicola than cinnamon and thyme in the drug sensitivity test. Moreover, essential oil fumigation inhibited the decay incidence of pitaya fruit inoculated with F. proliferatum and C. fructicola during storage at 4℃ and carcanol showed the best effect. Carcanol oil seemed to be a promising potential fumigant. The results can provide reference for disease control during storage of red pitaya in Zhejiang Province.