Grape pomace (GP), a winery by-product is increasingly being explored as food ingredients. Ochratoxin A (OTA), a natural toxigenic metabolite frequently found in wine and its by-products. Black Aspergilli<em> </em>are mainly responsible for OTA build-up and contamination of grapes and winery by-products. The fungal population in GP of five grape cultivars were enumerated and characterized. Fungal population ranged from 4.27±0.05 to 5.35±0.04 Log CFU/mL with GP from Chardonnay being the most contaminated.<em> Aspergillus niger</em> (81.1%) was found to be the major source of contamination and most frequently isolated fungal species. Other fungal isolates were <em>A. carbonarius </em>(13.51%) and <em>A fumigatus </em>(5.39%). Fungal contamination of GP correlated with the type of grape cultivars used for the pomace. Fourteen identified mold isolates were confirmed by PCR using primer pairs ITS1/NIG, ITS1/CAR and ITS1/FUM. Random amplified polymorphic DNA (RAPD) analysis with eight primers OPC-04, OPC-06, OPC-08, OPC-10, OPC-11, OPC-12, OPC-13 and OPC-14 revealed similarity in band patterns between the isolates and the control. Clustering of banding patterns generated from amplification with primer OPC-12 using Pearson’s coefficient detected similarity at 99.10%, 97.60%, 86.30% and 99.40%, 99.10%, 87.60%, 78.50% among <em>Aspergillus niger</em> and <em>Aspergillus carbonarious</em> strains, respectively, confirming the identification of potential ochratoxigenic black <em>Aspergillus</em> strains in the GP. The findings from this study suggest that GP obtained from some grape cultivars could be unsafe as food ingredients due to contamination by ochratoxigenic-producing molds, which is an indicative factor for the presence of ochratoxin A and other mycotoxins.