| A plenty of non-coding RNAs (ncRNAs) have been identified through the application of high-throughput analysis of the transcriptome, and this has led to an intensive search for possible biological functions attributable to these transcripts. In this study, the gonad tissue of the two-year-age Crassostrea gigas of same family cultured in Rizhao Huanghai area were used to identify a large number of miRNA, lncRNA and circRNA by small RNA-seq and RNA-seq , and their biological characteristics were analyzed. The results showed that, with Danio rerio as a reference, 25-30 known miRNA matures and 51-63 known miRNA hairpin was obtained, 53-71 new miRNA matures and 53-77 new miRNA hairpin were predicted. The length of miRNA in C. gigas ranged from 18-26 nt, where the largest number was in the 20-22 nt and the first nucleotide position was tent to U. 2302-2349 known lncRNA transcripts were obtained, and 20083-24114 new lncRNA were predicted. Among them, the percentage of the intergenic lncRNA, intronic lncRNA and antisense lncRNA was 29.0%, 62.1%, and 8.9% , respectively. The data showed that genomic characteristics of lncRNA in C. gigas were similar to those of other eukaryotes. Compared with mRNA, the transcript and open reading frame of lncRNA was much shorter at length and much lower at expression level. 383 circRNA transcripts were obtained, among which the average percentage of 88.54% came from exon, 4.51% came from intronic and 6.95% came from intergenic. The data showed that the endogenous circRNA have a lot miRNA target sites. This study showed that the basic biological characteristics of miRNA, lncRNA and circRNA in C. gigas. The results set the foundation for the subsequent research on the expression and biological function of regulatory non-coding RNA in C. gigas.