Corn and wheat flours are a significant part of the daily diet for millions of people. This work aimed to detect all the fungal flora associations and determine the mycotoxin production in the local corn and wheat flours. These samples were analyzed for mycoflora contaminant using (PDA) method and tested for mycotoxins production by using HPLC technique. The results indicated that, total fungal counts yielded 138 isolates belonging to 40 isolates from corn flour samples, equal to 29%, and 98 isolates from wheat flour samples, equaling 71%. Location (Z) gave a higher total fungal count with corn flour samples which recorded 34 isolates, equal to 85%, followed by location (A), which gave six isolates, equal to 15%. corn flour samples i.e. Aspergillus niger, A. flavus, A. parasiticus, Fusarium moniliform and Penicillium spp. wheat flour samples i.e. Alternaria alternate, Aspergillus niger, A. flavus, A. parasiticus, Fusarium moniliform, Penicillium sp., and Rhizopus stolonifer. Detection of mycotoxins presented that, only aflatoxins were produced by some isolates of A. flavus and A. parasiticus. From wheat flour, A. flavus isolate No. A/N/ 5 gave 0.59 ng/g of total aflatoxins, A. flavus isolate No. A/N/ 6 gave 0.71 ng/g of total aflatoxins and A. parasiticus (isolate No. A/N/ 94) gave 0.66 ng/g of total aflatoxins respectively. From corn flour, only Aspergillus flavus No. Z/N/ 22 which isolated gave 0.81 ng/g of total aflatoxins.