Shell coloration is one of important traits for genetic breeding, for improving genome structure and explore new potential gene and further determine the genetic structure of golden shell gene of oyster, the transcriptome sequencing of Crassostrea angulata with black shell and golden shell mantle were performed by Illumina platform. Data were obtained from black shell and golden shell transcriptome were 5 857 718 092 nt and 6 727 447 326 nt respectively, out of which 58 004 560 and 66 614 854 clean reads were remained after screening, respectively. To compare with the database from COG, GO, KEGG, Swiss-Prot and NR, new gene numbers corresponding to each database were 147, 397, 203, 567, and 1 347 respectively. To further explore the shell color genes of oyster, functional annotation, clustering analysis and screening from the reported shell matrix proteins on the differential expression gene (DEGs), 14 genes related to shell color expression were identified out and 5 down-regulated genes out of them might be related to the expression of golden shell.