The determination of geographical origin is a demand of the traceability system of import-export foodstuff. One hypothesis of tracing the source of a product is by analyzing in a global way the microbial communities of the food and links statistically this analysis to the geographical origin of the food (El Sheikha et al., 2009a). Physalis is included in the priority list of many governments¿ horticulture and fruit export plan. It is exported from several countries including Colombia, Egypt, Zimbabwe and South Africa, but Colombia stands out as one of the largest producers, consumers and exporters. Colombia exports of Physalis in 2004 were worth 14 millions USD (El Sheikha et al., 2008). In Egypt, economical importance of Physalis is rising, due to, achieving a great success in local, Arabic and European markets (El Sheikha, 2004). Physalis as the whole plant has many medicinal properties, including antipyretic, depurative, diuretic, pectoral, and vermifuge. A decoction is used in the treatment of abscesses, cough, fevers or sore throat (Duke and Ayensu 1985). The pulp is nutritious, containing particularly