The aim of the present study was to assess the prevalence and pathology of Lernaeid parasites in Schizocypris altidorsalis (Anjak Fish) fish from Chahnimeh lakes and Hamoun wetland in Sistan and Baluchestan, Iran. A total of 1000 S. altidorsalis fish were collected from October 2014 to September 2015. The prevalence of Lernaea spp. infestation in examined fish was found to be 61.1% (611/1000). Among the examined weight groups, the highest infestation rate (61.7%) was recorded in the weight group of 80-100g, followed by 60.5% and 58.7% in 100-150g and 150-200g weight groups, respectively (P>0.05). The frequency of Lernaea spp. in winter (75.2%) was higher than other seasons and the lowest prevalence was observed in summer (38%). The association between the season and the prevalence of Lernaea spp. infestation was statistically significant (P<0.001). The histopathological examination of the sections revealed lesions and ulcers in the epidermis, dermis, and muscles of the fish. Chronic inflammatory reaction and infiltration of inflammatory cells including lymphocytes, plasma cells, macrophages, and eosinophils around the parasite attachment sites were observed. In severe cases, various degrees of degeneration and necrosis were seen in the muscle. The present survey revealed a high prevalence of Lernaeid parasites in S. altidorsalis fish and necessitates appropriate control programs.