With the ever-increasing pace of urban life, many people now rely a lot on processed foods. Some of these processed foods are prepared hygienically and yet some are prepared in homestead and brought to the open market, without having gone through any microbial quality checks. This has in the recent past led to outbreaks of food -borne diseases such as Cholera and Salmonellosis to mention a few. In this study, processed food samples were collected from three open markets in Windhoek namely Single quarters, Soweto market and the Okuryangava Bus stop. The samples included maize (flour), dried Cleome gynandra leaves, mopane worms, roasted groundnuts, minnos, and cooked beef steaks. Morphological identification was done based on the macroscopic characters based on the colour, shape, and texture and microscopic characterization using lactophenol cotton blue wet mount. DNA was extracted from the fungal isolates and PCR was performed using ITS1 and ITS4 primers. The PCR products were sequenced, and the results were used for identification using the BLAST search program in NCBI. Dried Cleome gynandra contained most of the isolated fungal species which were identified Pichia burtonii, P. macrostoma, Dothidealus, and A. parasiticus. However, Aspergillus species were present in all the food samples and A. parasiticus was found in all food samples except the ground nuts. These could be an indication of that the fungus prefers low water activity and possibly high salt concentrations to survive.