In this study, genetic analysis was performed for five new red body color bream mutants (two males and three females) from the natural environment. By measure countable morphological traits, the soft ray number of dorsal fin, the spine number of dorsal fin and anal fin in red color bream mutants are 14, 2 and 2 respectively, whereas those in other 6 Megalobrama and Parabramis species (M. terminalis from Dong river, M. terminalis from Qiantang river, M. hoffmanni, M. amblycephala, M. pellegrini and P. pekinensis) are 16-19, 3 and 3, respectively. Principal component analysis show the red color bream mutants have a close relationship with M. amblycephala based on 9 measurable proportion parameters and 20 frame parameters. Microsatellites analysis demonstrated that the red color bream mutants and M. amblycephala firstly grouped together, and their genetic distance was 0.3094. The genetic distance between the red color bream mutants and P. pekinensis was 3.7439, which was the farthest. Finally, the genetic similarity between the red bream mutants and M. amblycephala, M. terminalis, P. pekinensis, Sinibrama macrops, Culter alburnus, Chanodichthys mongolicus, Carassius auratus, Cyprinus carpio and Danio rerio are 99%,95%,95%,94%,94%,93%,86%,86% and 82% respectively, by sequence analysis from mitochondria COX1 and COX2 genes. Cluster analysis results also show the highly close relationship between the red bream mutants and M. amblycephala, indicating the red body mutants may have originated from M. amblycephala. The red M. amblycephala could provide valuable materials for future genetic breeding of M. amblycephala.