In sampling of Siniperca fishes from Poyang Lake and Dongting Lake in the middle Yangtze River, 48 intermediate individuals with partial morphological features of S. chuatsi and S. kneri (Main feature:The posterior edge of the cleft mouth is below the posterior edge of the eye, the eye size and the anterior ridge of head are between the S. chuatsi and S. kneri) were collected. In order to clarify their taxonomic relationship, the quantitative morphological parameters and species-specific microsatellite loci were screened for identification. Results showed:(1) there was significant difference in head length/eye diameter and (snout length+eye diameter)/fissure length between S. chuatsi and S. kneri. Head length/eye diameter in S. chuatsi is from 5.286 to 7.157, (snout length+eye diameter)/fissure length is from 0.811 to 0.999, they are from 3.306 to 5.106 and 1.040 to 1.166 in S. kneri, respectively. Among 48 intermediate individuals, 5 individuals were identified as S. chuatsi, and the remaining 43 individuals were still unable to be identified. (2) Five speices-specific loci (T103, T063, T089, T135, W19517) were screened from 28 pairs of microsatellite markers. In genetic analysis and identification of intermediate types of individuals using these five loci, 16 were inter-species hybrid progeny, and 9 of them were identified as backcross progeny (F₁×SK). The results indicated that inter-species introgressive hybridization between S. chuatsi and S. kneri existed in the middle Yangtze River, and it is necessary to strengthen genetic monitoring and management of mandarin fish resources in the Yangtze River.