Gonadal transcriptome sequencing was performed using RNA-seq technology on the trioecy population of Corbicula fluminea(male, female, and hermaphrodite) collected from the Yuanjiang River in Hunan Province. Differentially expressed genes(DEGs) were screened under the Padj(adjusted P)<0.05 and |log2FC|>1(FC as fold change). After Gene Ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) functional enrichment analyses, candidate genes related to gonadal development were selected and further validated by quantitative real-time PCR(qRT-PCR). The results showed that a total of 562 386 high-quality transcripts were obtained, and 213 504 differentially expressed genes(DEGs) were identified through comparative analysis of nine gonadal transcriptome libraries from three sexual phenotypes. GO enrichment analysis indicated that these DEGs were related to motile cilia, microtubules, cell division, and microtubule binding. KEGG pathway analysis revealed that the DEGs were primarily enriched in cellular senescence, the p53 signaling pathway, oocyte meiosis, progesterone-mediated oocyte maturation, and cell cycle. From the transcriptome dataset, nine candidate genes associated with gonadal development and sex differentiation were identified, including Vom1, Tssk, Fem-1, Spag17, Spata7, Spag8, Tepp, Sfp2 and Spag6. Among them, Tssk, Spag17, Spata7, Spag8, Tepp, Sfp2, Spag6 and Fem-1 exhibited significantly higher expression levels in male gonads than those in female gonads. Seven of the eight candidate genes were verified by qRT-PCR, and the expression trends were generally consistent with the transcriptome results. It is speculated that Fem-1 may play a regulatory role in sex determination or differentiation, while Tssk, Spag17, Spata7, Tepp, Sfp2, Spag6 and Spag8 are potentially involved in spermatogenesis, and Vom1 may be involved in ovarian development.