Development of shrimp farming has been associated with the incidence of fatal diseases including viral, bacterial and protozoan parasites of shrimp. Our study was aimed to present an status of several important protozoan parasites of F. indicus in cultured earthen ponds in Iran during the period of 2011 to 2012. One hundred live shrimp  were randomly prepared from the Shrimp Helleh Station in south of Iran. Prevalence and intensity were two important indices that calculated in our research. They were scraping, putting on clean slides and examined under microscope to observe the protozoan parasites. Zoothamnium sp. is more prevalent pathogen among peritrichous ciliates (88.66% to 79%) in pleopods. Acineta sp. was less prevalent in our isolations neither in pleopods nor in gills. It is concluded that, peritrichous ciliates are more frequent ciliates causing mortality in cultured shrimps at high density in higher temperature and ammonia.