Chalcalburnus mossulensis from the cyprinidae family is one of the indigenous fish in Gheshlagh Lake of Kordestan, Iran. Ligula intestinalis is one of the infective parasites among various species of fish and causes gonads atrophy. In this study, after detection of species and age of samples, the effects of this parasite on gonads tissues and sexual maturation of Chalcalburnus mossulensis were investigated. By seasonal sampling 144 samples were collected. After investigatiing gonad tissue samples, it was clear that, there is a significant difference between the means of male and female gonads maturation rate in infected and non infected samples (p< 0.05). Infection by Ligula intestinalis can be the reason for lack of gonads maturation. In addition, the abnormal degenerative changes like, absorption follicle, hemorrhage and infiltration of inflammation cells in ovary tissues of infected fish were seen. In testicle tissue, dispersed hemorrhage, atrophy and MMC (melano-macrophage center) were seen as pathological signs. So the spread of this parasite in different water sources is important as the point the maintenance of native species and cultivated fish.