Background: The aim of this study was to detect the occurrence of parasites in fish in Armand River, CHAHARMAHAL va BAKHTYARI PROVINCE regarding the importance of native fish population in the river.Methods: The occurrence of parasites was investigated in 6 native fish (Capoeta capoeta, C.damascina, C. aculeta, Barbus barbulus, B. grypusand Glyptothorax silviae) collected from the current main channel of the river from autumn 2009 to summer 2010.Results: 63.7% of the studied fishes were infected with 19 parasite species including Ichthyophthirius multifiliis, Myxobolus musayevi, Dactylogyrus lenkorani, D. gracilis, D. pulcher, D.chramuli, D. akaraicus, D. skrjabiensis, two species of Gyrodactylus, Paradiplozoon sp., Lamproglena compacta, Copepodid of Lernaea cyprinacea, Ergasilussp., Allocreadium isoporum, Allocreadium pseudaspii, Kawia sp., Bothriocephalus gowkongensis and Rhabdochona denudata.The infection rate was significantly higher (P<0.05) in C.aculeata while the maximum parasite diversity was found inC.damascina. The infection rate was also significantly different in four seasons (P<0.05) but no significant differences were found among fishes with different weight and length.Conclusion: High prevalence of Ichthyophthirius multifiliis and Rhabdochona denudata may affect native fish population. Monogenean parasites Dactylogyrus akaraicus and D. skrjabiensis collected from B. barbulus and C. capoeta are reported for the first time in Iran. B. barbulus is also reported as a new host for aforementioned parasites.