Seedless barberry (Berberis vulgaris L. var. asperma) is one of the few unique crops grown only in Iran and southkhorasan. Barberry is a well known medicinal plant in Iran and has been widely used as food additive. The comprehensive survey of fungal contamination of barberry was undertaken in the market of Birjand, during March to June at 2012. Fungal infections of barberry were studied in thirty samples. Among these, Aspergillus spp., Penicillium spp. and Mucor spp. were major contaminants also the results showed that 57% of barberry was infected and most fungal species related to Aspergillus spp. and penicillium spp. Therefore it needs to undertake the management practices.