Abstract: Since morphology and body spots characteristics are important breeding traits in mandarin fish crossbreeding, we analyzed the difference in quantifiable morphological traits of the backcross progeny S. scherzeri ♀× (S. scherzeri ♀×S. chuatsi ♂) and parental offspring (S. scherzeri, S. scherzeri ♀×S. chuatsi ♂) by multiple comparison, hybrid index, principal component analysis and discriminant analysis, and observed the body spots of the backcross. The results show that the average hybrid index of the backcross was 38.73. The morphometric difference analysis and hybrid index indicate that the backcross progenies were biased toward S. scherzeri. Principal component analysis and discriminant analysis reveal that the main differences lay in head angle, body height/body length, head height/head length, and C (the length from the back of the angle bone to the beginning of the ventral fin)/body length between the backcross progenies and their parents. The three-dimensional spatial distribution of the backcross, S. scherzeri and the hybrid on the first three principal components did not overlap and were distinguished from each other. Discriminant analysis can clearly classify the three groups in two-dimensional. The body spots of the backcross included back saddle spots and trunk spots which can be classified into four different combinations. 45.5% of the individuals had back saddle spots, and 72.8% had hollow spots. The results can provide data for cross breeding and hybrid identification of mandarin fish.