Anjak (Schizocypris altidorsalis), is a native benthopelagic and commercially important fish species in Hamun Lake and Hirmand River system in Sistan basin, Iran (Coad and Ville, 2005 Jami et al., 2015). Together with snow trout (Schizothorax zarudnyi), anjak make up the most favourite source of animal protein for Sistan residents. It belongs to the family Cyprinidae and sub-family Schizothoracinae, which are widely distributed in the Himalayan and sub-Himalayan region and the rest of Asia (Jami et al., 2015). Almost nothing is known about the nature and biodiversity of intestinal microbiota in this fish. Hence in this study the composition of the gut bacterial communities in the anjak was surveyed by 16S rRNA gene 454-pyrosequencing.