Under certain storage conditions, some fungi such as Aspergillus, Fusarium, Penicillium, Alternaria species can cause spoilage in stored crop seeds, decreasing crop value, or produce mycotoxins that have a direct effect on human health. Protecting stored wheat grain from fungal spoilage is an essential part of their production. Wheat associated microorganisms can have beneficial effects on the stored grain`s health. Understanding the composition and role of stored wheat grain microbiota is crucial toward agricultural practices that are less dependent on chemical fungicides, which has known negative effects on the environment and human health. In the present study, we used 16S and 18S rRNA high throughput sequencing to explore stored crop seeds microbial communities and also obtained a large number of bacterial and yeasts isolates from epiphytic and endophytic microflora of wheat grains, which are being assessed for their antifungal activity in-vitro. Preliminary results indicate that some of the screened isolates presented antagonistic properties toward mycotoxigeneis pathogens such as Aspergillus flavus and Alternaria species. Yet, the complexity and diversity of native microbial communities associated to stored wheat grain are still unclear and should be further investigated.