Seed is the basic and most important structure through which majority of crops are grown. To increased produce, there is need for viable seeds and proper preservative measures which prevent the seeds from attack by fungal pathogens, thus enabling germination and increased productivity. It is to this effect a study was carried out to investigate the occurrence of Aspergillus species in maize seeds obtained from Konshisha Local Government Area of Benue State and the use of plant extract to control the seed borne fungi. The study was conducted at the Botany Laboratory of the Department of Biological Sciences, Benue State University, Makurdi. A total of five markets namely; Agia, Ati, Awajir, Koryan and Shiliki were used for the collection of maize samples. A total of Four hundred and fifty seeds (360) were collected across the five locations and were analyzed for seed borne infection. The blotter method of fungal detection and isolation was employed for the study. Neem leaf extract was prepared at different concentration of 10, 20, 30, 40 and 50% w/v for the in vitro control of fungi isolated. The result obtained showed the presence of two Aspergillus species namely; Aspergillus flavus and Aspergillus niger. There was no significant difference in the occurrence of A. flavus among the markets assessed. Although, the highest value was recorded in Ati market. Percentage occurrence of A. niger was significantly high at (P?0.05) in Koryan markets compared with Ati and Awajir markets. Values for shiliki and Agia were not different from that of koryan but were also significantly (P?0.05) higher compared with Ati which had the lowest occurrence of A. niger. There was no significant difference recorded across the five markets as regards percentage seed germination. Neem leaf extract was effective in inhibiting radial mycelia growth the test fungi. Radial growth inhibition at 50% w/v was significantly higher (P<0.05) compared to other concentrations. The use of Neem leaf extract can be used to control the growth of these fungi on maize seeds in storage and also enhance their germination potential. Therefore government should establish industries for the seed treatment of crops with plant botanicals as this will help reduce the amount of money spent on synthetic fungicides.