Maize (Zea mays L.) is a cereal crop grown throughout the world. Invasion of maize grains by fungi leads to losses in quantity and quality. The objective of the current study was to assess the diversity of fungi associated with stored maize grains under storage conditions of farmers in Shashemene and Arsi Nagelle districts. Stratified random sampling technique was used to collect maize grains from the study sites of Arsi Nagelle and Shashemene districts. Two peasant associations (PAs) from each district and 10 HHs from each of the PAs, with a total of 40 HHs were purposively drawn for sample collection. A 2% MEA and PDA plates were used for the isolation of fungi associated with the collected maize grains. Identification of the isolates to the genus level was performed on the basis of culture characteristics and spore morphology. A total of 767 fungal isolates belonging to ten genera and four unidentified taxa were obtained. Out of which 430 (56.06%) were from Shashemene and 337(43.94%) were from Arsi Nagelle. In general comparison, higher isolation rate (IR) was found at Shashemene than Arsi Nagelle. While, in case of Arsi Nagelle districts higher number of fungal isolates was at Ali Wayo 172 (22.43%) than Adaba Tita 165 (21.52%). Aspergillus spp. was the dominant that were represented by 284(37.027%) isolates from all sites. Penicillium was the second most frequently encountered genus where 196(25.55%) isolates was recovered from all sites. It was concluded that stored maize grain from the study areas could be contaminated by storage fungi and therefore, awareness creation and training should be given to the farmers on better and improved storage techniques.