Fungi produce a series of toxic compounds on corn, especially Fumonisin B1 (FB1) toxin produced by Fusarium spp. and promoting cancer activity in humans and animals. This study aimed to the isolation and identification of fungi associated with local corn seeds and the detection for the presence of FB1 by using ELISA technique. Thirty samples of corn ears were collected from silos and markets in Baghdad city during the period from November 2018 to March 2019. The present study found that Fusarium was the dominant isolate among fungi in terms of the relative density 57.07%, followed by Aspergillus 31.17%, Rhizopus 3.36%, Alternaria 2.88%, Mucor 2.16%, Penicillium 1.92%, Trichothecium 0.96%, and Helminthosporium 0.48%. FB1 was detected in all samples of the silos and markets with a concentration range of 13.69 - 175.54 µg/kg. There were no significant differences in FB1concentration among samples collected from the silos and markets. Also, no relationship was found between the number of infected seeds by Fusarium spp. and FB1concentrations.