Aflatoxigenic fungi like Aspergillus spp., commonly contaminants food, which has different methods to detect their presence. The early detection of food contaminants is quite significant to prevent the hazard on the human health and economic. This study aims to detect the isolation and diagnosis of the companying fungi from some nuts that are available in local markets of Babylon province (Iraq) and explore their ability to produce aflatoxins. The Aspergillus spp., was the most common, followed by each of the Cladosporium spp. and Penicillium spp. The results from isolation and diagnosis of this study showed that Aspergillus flavus was the most visible fungus in all kinds of examined nuts. The highest rate of appearance for this fungus was in pistachios, reaching 70%, whereas the rest of kinds of nuts ranged between 60-10%. The Polymerase Chain Reaction (PCR) technique was utilized for the diagnosis of A. flavus by using a special primer. In this study, the PCR technique was used for the detection of Aflatoxigenic A. flavus and ammonia chemical detection was used to compare this technique.