Plant extracts are a valuable alternative for the control of phytopathogenic fungi in horticultural crops. In the present work, the in vitro antifungal effect of ethanol and aqueous extracts from different vegetative parts of 40 native plants of the Yucatan Peninsula on Curvularia lunata ITC26, a pathogen of habanero pepper (Capsicum chinense), and effects of the most active extracts on postharvest fruits were investigated. Among these, the ethanol extracts of Mosannona depressa (bark from stems and roots) and Piper neesianum (leaves) inhibited 100% of the mycelial growth of C. lunata. The three extracts were partitioned between acetonitrile and n-hexane. The acetonitrile fraction from M. depressa stem bark showed the lowest mean inhibitory concentration (IC50) of 188 µg/mL against C. lunata. The application of this extract and its active principle α-asarone in the postharvest fruits of C. chinense (500 µg/mL) was shown to inhibit 100% of the severity of the infection caused by C. lunata after 11 days of contact. Both samples caused the distortion and collapse of the conidia of the phytopathogen when observed using electron microscopy at 96 h. The spectrum of M. depressa enriched antifungal action is a potential candidate to be a botanical fungicide in the control of C. lunata in cultivating habanero pepper.