The crucian carp (Carassius auratus) is an economically important freshwater fish species in China, widely distributed throughout the Haihe River Basin. It is one of the main species released in the area. To assess the current status of population diversity of C.auratus in different rivers within the basin and standardize stock enhancement practices, this study collected 170 individuals from six populations in Guanting Reservoir (three populations from Guishui River, Sanggan River and Woniushan), Juma River (one population from Qianhekou) and Panshitou Reservoir (local and released populations). A total of 16 morphological traits and 5 morphometric ratios were measured for cluster analysis. Microsatellite markers were used to analyze genetic diversity and genetic distances among populations. The results showed that snout length, caudal peduncle length, and caudal peduncle depth were significant different (P<0.05) among populations from Guanting Reservoir, Juma River and Panshitou Reservoir. Snout length and caudal peduncle depth were significant different (P<0.05) among the Guishui River, Sanggan River and Woniushan populations within Guanting Reservoir. Between local and released populations of the Panshitou Reservoir, significant differences (P<0.05) were found in body depth, eye diameter, caudal peduncle length and caudal peduncle depth, while extremely significant differences (P<0.01) in mouth cleft size, mouth shape and relative intestine length. The results of morphological Euclidean distance cluster analysis showed that the three groups of Guanting Reservoir (Guishui River, Sanggan River and Woniushan) first cluster into one branch, and then cluster with the Qianhekou population of Juma River. The Euclidean distance is closer to the Woniushan group of Guanting Reservoir. The populations in Panshitou Reservoir clustered separately. The released population in Panshitou Reservoir has less similarity with other groups. Generally, there are two main branches totally. Through sequence identification, the 5 individuals from local population in Panshitou Reservoir had 97% - 98% of their mitochondrial DNA matching that of Silver Carp (Carassius gibelio), 96% - 98% matching the hybrids of Yellow River Carp and Blackhead Carp (Megalobrama amblycephala). Among the 10 individuals of released population, 2 with whiskers had a 98% match with the mitochondrial DNA of Yellow River Carp, while the other 8 without whiskers and had a 92% - 95% match with the mitochondrial DNA of Yellow River Carp (Cyprinus carpio haematopterus). Three individuals of Qihé Carp (Carassius auratus var. Qíhé) had a 98% match with Silver Carp. The degree of genetic variation at 7 microsatellite loci within the same population and at the same microsatellite locus among different populations varies greatly. The results of genetic diversity indicated that the genetic distances of the crucian carp populations in Guanting Reservoir, Juma River and Panshitou Reservoir reached the standard for geographical species division (greater than 0.05). The genetic relationship between the Guishui River population and the Sanggan River population in Guanting Reservoir was relatively close, with a genetic distance of 0.0193. The genetic relationship between the Guishui River population and the Woniushan population was slightly farther, with a genetic distance of 0.0459. Overall, the morphological and microsatellite-based cluster analyses yielded consistent results, demonstrating distinct population differences among tributaries within the Haihe River Basin. It is suggested that cross-basin water system releases have potential ecological risks and the source control of seedlings for restocking needs to be further improved to provide strong support for scientific resource conservation in each basin.