Fruit and vegetable products are susceptible to the attack of fungi during postharvest handling. Chemical fungicides are the most commonly used technique to control fungal diseases. However, an alternative product is the use of plant extracts, which have been reported in in vitro and in vivo conditions. The objective of this investigation was to identify one of the main pathogens of mango and soursop fruits using morphological and molecular tools as well as to evaluate the in vitro inhibitory effect of papaya and soursop leaf and seed extracts. Two pathogens were isolated and identified by their morphological and molecular characteristics from mango and soursop fruits. We obtained extracts from leaves and seeds of soursop and papaya using five solvents of increasing polarity (hexane, acetone, ethanol, methanol, and water) through the ultrasound-assisted extraction technique at a frequency of 35 kHz and 160 W for 14 min. In vitro evaluations of the extracts were performed using the Kirby-Bauer technique. The extracts with the highest percentage of inhibition were analyzed qualitatively and quantitatively using standardized techniques of colorimetry and spectrophotometry. Furthermore, we determined the content of total phenols, flavonoids, alkaloids, terpenoids, anthraquinones, coumarins, and saponins. As a result, we identified the pathogens as Colletotrichum fructicola and Nectria haematococca. Aqueous extracts (water as a solvent) showed a higher percentage of inhibition of both pathogens compared with the other extracts. Furthermore, the aqueous extract of papaya leaf was the most effective among all extracts. The aqueous papaya leaf extract exhibited a percentage of inhibition of 49.86% for C. fructicola and 47.89% for N. haematococca. The aqueous extracts of papaya leaf and seed (AqEPL and AqEPS) presented the greatest amount of metabolites (except anthraquinones and coumarins). The aqueous soursop leaf extract (AqESL) presented the greatest amount of phenols, tannins, and flavonoids (219.14 [+ or -] 8.52 mg GAE/L, 159.84 [+ or -] 10 mg GAE/gdm and 0.13 [+ or -] 1.12 * [10.sup.-4], respectively). The aqueous soursop seed extract (AqESS) had the highest saponin content with 1.2 [+ or -] 0.1 mg QSES/g dm and the papaya leaf accusative extract (AqEPL) had the highest alkaloid content (6.413 [+ or -] 1 * [10.sup.-3] mg AE/g dm) compared with the other extracts. The AqESS had a lower content of secondary metabolites (sterols, alkaloids, and saponins), while AqESL showed no presence of alkaloids and coumarins.