Deformities in cultured fish species may be genetic, and identifying causative genes is essential to increase production and maintain farmed animal welfare. In this analysis, transparent phenotype of juvenile red sea bream (Pagrus major) was focused. We produced an experimental family, and normal phenotype and transparent phenotype were obtained. Genome-wide linkage analysis was conducted by ddRAD-Seq method using the experimental family. SNP-based linkage maps were also developed.