Corn and wheat flours are a significant part of the daily diet for millions of people. This work aimed todetect all the fungal flora associations and determine the mycotoxin production in the local corn and wheatflours. All corn and wheat flours were packed in 50kg bags as commercial presentations of each type. Sampleswere collected from three localities area. These samples were analyzed for mycoflora contaminant using thePotato dextrose agar (PDA) method and tested for mycotoxins production by using HPLC technique for theseparation process. The results indicated that, total fungal counts yielded 138 isolates belonging to 40 isolatesfrom 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 bylocation (A), which gave six isolates, equal to 15%. Corn flour samples collected from location (B) were betterthan others which recorded zero fungal flora percent. On the other hand, location (B) was the most total fungalcount isolated from wheat flour samples which record 60 isolates equal 61.2% followed by location (A) whichgave 32 isolates equal 32.7% and location (Z) which record 6 isolate equal 6.1%. Five fungal speciesbelonging to three fungal genera were identified from different corn flour samples i. e. Aspergillus niger, A.flavus, A. parasiticus, Fusarium moniliform and Penicillium spp. Aspergillus flavus was the most fungalfrequency occurred. Whereas seven fungal species belonging to five fungal genera were identified fromdifferent wheat flour samples. These are Alternaria alternate, Aspergillus niger, A. flavus, A. parasiticus,Fusarium moniliform, Penicillium sp., and Rhizopus stolonifer. Detection of mycotoxins presented that, onlyaflatoxins were produced by some isolates of A. flavus and A. parasiticus. From wheat flour, A. flavus isolateNo. 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 aflatoxinsand 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. Fumonisin B1 was not detected