Abstract A survey of some fungi associated with onion bulbs rot was carried out in Maiduguri, Borno State Nigeria. The aim of the study was to isolate and identify the fungal pathogens that cause the onion bulb rot. Onion samples were collected in three markets within Maiduguri, namely, Gamboru, Monday market and Baga markets. Four fungal pathogens were identified as Aspergillus niger, A. Flavus, Botrytis aclada and Penicillium expansum. Pathogenicity test conducted indicated that all the isolates were pathogenic on onions, thus causing rot. However, A. niger was the most virulent of the other isolates with highest mean rot diameter of 40.0 mm and P. expansum least virulent with only mean rot diameter of 21.00 mm. A. niger was prevalent in Gamboru market (96%), Monday market (90%) and Baga (75%), while least encountered was P. expansum with disease incidence of (45%) in Baga and Monday market respectively. Three plant extracts were tested on the organisms isolated. Of these plant extracts experimented. Mahogany leaves extract was highly effective against the organisms than the other plants extract and affordable compared to the pesticides which are poisonous and costly.