Background The goosehead red goldfish (Carassius auratus) is a typical representative of Beijing court goldfish. Long-term artificial selection and regionalized aquaculture may have led to morphological differentiation among different populations, but systematic morphological comparative studies are currently lacking.

Objective This study aims to quantify the morphological differences among three cultured populations of goosehead red goldfish, screen key discriminant traits, and construct an effective population discrimination model.

Methods A total of 90 individuals from three major aquaculture farms were used as research subjects, and ten morphological traits (body length, body width, body depth, head length, snout length, eye diameter, interorbital distance, tail length, caudal peduncle length, and caudal peduncle depth) were measured. Multivariate statistical methods including one-way ANOVA, principal component analysis, cluster analysis, and stepwise discriminant analysis were employed for comprehensive analysis of morphological differences in three cultured populations of C. auratus.

Results The three cultured populations of C. auratus exhibited significant differences (P < 0.05) in several morphological traits, including body width/body length, snout length/body length, and caudal peduncle length/body length. The first two principal components extracted by principal component analysis accounted for 72.57% of the cumulative variance, primarily reflecting body shape, head, and tail characteristics. Cluster analysis results showed that the Euclidean distances among three cultured populations of C. auratus were similar, and they were generally at the same similarity level. Stepwise discriminant analysis screened six key traits (body depth/body length, body width/body length, snout length/body length, eye diameter/body length, caudal peduncle length/body length, caudal peduncle depth/body length), and the established Fisher’s discriminant function achieved an overall discriminant accuracy of 85.60% for three cultured populations of C. auratus.

Conclusion Different cultured populations of C. auratus have developed significant and quantifiable morphological differentiation under artificial selection. The constructed discriminant function has high practical value and can provide a scientific basis for germplasm identification, selective breeding, and market traceability of C. auratus.