The fruit of Ficus sycomorus holds significant economic value in Nigeria. It offers a myriad of medicinal advantages, including the treatment of jaundice, snake bites, dysentery, chest pain, cough, and throat infections. Despite the plant's importance, it has been noted that the shelf-life of its fruits is compromised by various diseases caused by fungal pathogens. A study was carried out to isolate and identify the prevalent fungal pathogen responsible for the decay of F. sycomorus fruits. Diseased fruits were collected from Okochiri in the Okrika Local Government Area of Rivers State and were identified morphologically. The DNA of the most frequently isolated fungi, coded FF2 9-7 and FF2 5-8, were characterized molecularly using Internal Transcribed Spacer (ITS-1 and 2) markers. The morphological analysis revealed that the FF2 9-7 and FF2 5-8 isolates belonged to the Pestalotiopsis and Dipodascus genera. The molecular weight of the isolate's DNA exceeded 500 base pairs. According to sequence similarity, the DNA sequence of the isolate was found to be 80.83% identical to that of the Pestalotiopsis mangiferae strain and 97.06% identical to Dipodascus sp. strain F1 E06. Consequently, these findings indicate that Pestalotiopsis mangiferae and Dipodascus sp. are the fungal pathogens responsible for post-harvest rot in F. sycomorus fruits. It is anticipated that these results will contribute to the development of effective disease management strategies aimed at reducing post-harvest losses attributed to these organisms, improve on the current information and aid in reducing the deteriorating activities of fungi invading fig-mulberry fruits while also laying the groundwork for further investigation into the potential mycotoxin effects of consuming infected F. sycomorus fruits.