Parasitic infestation of two native fish species in Behesht-Abad River were investigated at spring 2013. In this study 52 Chondrostoma regium and Aphanius vladykovi (26 from each species) were sampled and transferred to the laboratory. Then the weight and total length of fish were measured and investigated their infestation to parasites by microscope and stereomicrpscope. Some of the observed parasites are reported for the first time as new host records of: Philometra sp on the abdominal cavity of C. regium, Moreover, some external and internal parasites identified to the species and genus level including: Ichthyophthirius multifiliis in skin and gill of C. regium and A. vladykovi, one immature digenean; Allocreadium isoporum on the intestine of A. vladykovi and Trichodina sp on gill and skin of C. regium and A. vladykovi. The highest frequency of I. multifiliis (96.15%) was observed in gill of A. vladykovi and the lowest frequency  was related to Tricodina sp in skin of C. regium (23.07%). A. isoporum Infestation was only observed in the intestine of A. vladykovi (mean±SD; 5.42±3.73) and philometra sp infection was only observed in the abdominal cavity of C. regium (mean±SD; 3.25±.82). The maximum average (±SD) infection intensity belonged to I. multifiliis in skin of C. regium (69.9±72.07, range: 12-196).