The current study aimed to investigate the occurrence of Cryptosporidium species by traditional and molecular methods in freshwater fish in Baghdad city. A convenient number of stomach and intestinal continent samples were collected from three types of freshwater fish from different areas of Baghdad city from November, 2023 to April, 2024. All samples were examined phenotypically using a modified Ziehl-Neelsen stain and genotypically (nested PCR technique) based on a partial sequence of 18SrRNA genes with sequencing and phylogenetic tree analysis. The overall infection rate of fish with C. parvum was 5.5% (10/180). The common carp (Cyprinus carpio) was the only fish type infected, with a rate of 16.66% (10 60). January and February had the highest infection rate, 3.33%. The molecular identification and sequencing confirmed the infections with C. parvum. Molecular speciation of the parasite confirmed microscopical primary identification results. This study suggests that fish became a new source for transmission to humans and livestock.