Juniperus procera and Avicennia marina extracts were tested for their antifungal activity against Curvularia lunata isolated from rice (Oryza sativa L.). Eextracts were able to supress C. lunata at high concentration 3 mg/ml. J. procera extract retarted the growth C. lunata by 88.42% while A. marina extract was less effective (37.50%). Nucleic acids content of C. lunata was reduced by both plant extracts especially J. procera extract in a distinct reverse proportion relationship when compared with the untreated samples. The antifungal effect of J. procera and A. marina extracts were explored at the molecular level, using random amplification of polymorphic DNA (RAPD). The results demonstrated polymorphic banding pattern. Secondary metabolites analysis of C. lunata revealed that both plants extracts were capable of blocking biosynthesis of some secondary metabolites including curvulalic acid and lunatin.