Noble scallop (Chlamys nobilis) is an economically important cultured marine bivalve shellfish common in southern China. Investigation on the molecular regulatory mechanisms of gonadal maturation in scallop is critical in the aquacultural industry. Here, gonads in maturing stage were obtained from noble scallops and sequenced using an Illumina high-throughput sequencer, producing 6.68 and 6.70 Gb of data for the ovary and testis, respectively. Reproduction-related genes, including vasa, nanos, and vitellogenin, and sex-determining genes, such as FoxL2, Dmrt, and sox9, were detected. Transcriptome comparison revealed 2,842 differentially expressed genes (DEGs), of which 591 exhibited biased expression in the ovary and 2,251 exhibited biased expression in the testis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of the DEGs were conducted. Results showed that GO terms and KEGG pathways related to protein glycosylation, fatty acid biosynthetic processes, hydrolase activity, and AMPK were enriched in the ovary, whereas those related to male organ formation and spermiogenesis were enriched in the testis. The glycosphingolipid biosynthesis pathway was identified for the first time in a mollusc testis.The present study provides the first transcriptomic analysis of C. nobilis, which will help clarify the molecular mechanisms of gonadal maturation.