Abstract: South Africa is an upcoming pomegranate producer and exporter in the Southern Hemisphere. The study highlights the importance of determining the etiology and potential of pomegranate postharvest pathogens using molecular techniques to ascertain when/where infection occurs to allow integrated management strategies to be implemented. High counts of Penicillium spp. and Alternaria spp. were observed from preharvest to commercial harvest time with limited fruit damage after fungicide treatment in the pack-house. Isolates of fungal pathogens causing fruit decay were plated on potato dextrose agar (PDA) and incubated at 25 °C for further microscopic and/or molecular identification. The casual agents of latent infection were Alternaria spp., Aureobasidium spp., Pilidiella granati, Penicillium spp. and Botrytis cinerea, respectively. Fungicide treatment in the pack-house reduced disease incidence significantly.