The aim of this study is to isolate, identify and confirm the microorganisms causing the fungi diseases of watermelon, determine the antimicrobial properties of ethanolic extract of Azadirachta indica and Vermoma ainagdalina and Zingibaz offIcinale on fungal diseases of watermelon e.t.c. The study was carried out to evaluate Azadirachta indica (Neem leaf) and Vernonia amygdalina (Bitter leaf) extract in the inhibition of fungi causing rot of watermelon (citrullus lanatus ). Watermelon belongs to the family cucuritaceae, which consist of nearly 100 genera and over 750 species. Watermelon is grown annually and can be up to 3meters long. They are widely distributed in the tropics and subtropics, and a few species occurs in temperate regions. The method employed was to isolate and identify the pathogens causing rot from watermelon. The fungi pathogen isolated were A. niger, ,S. cerevisiae , A. wentii. The fungi were cultured with the neem and bitterleaf extracts using potato dextrose agar and mycelia growth and zone inhibition was observed. V. amygdalina and A.indica have inhibitory potential on post harvest rot causing fungi of watermelon and suggest it’s ability to prolonging its shelf life and prevent diseases. For the result, three fungi were isolated and identified which includes Aspergillus niger, Aspergillus wentii, Sacharomyces cerevisiae. Pathogenicity confirmed that the isolated fungi were the casuative agent of the rot. A. niger colonies appear black in PDA plates, which was initially white and later turned black. Under the microscope the mycelia is separate, conidiophores are long with vesicle like tips. In conclusion, all the tested fungal isolates were responsible for decay of watermelon fruits. The same isolates contaminate fresh cut ready to eat watermelon fruits, this shows that they used compromised surfaces of their fruits such as wounds to cause rots.