| Summary: | <i>Diodon hystrix</i> is a new and emerging aquaculture species in south China. However, due to the lack of understanding of reproductive regulation, the management of breeding and reproduction under captivity remains a barrier for the commercial aquaculture of <i>D. hystrix</i>. More genetic information is needed to identify genes critical for gonadal development. Here, the first gonadal transcriptomes of <i>D. hystrix</i> were analyzed and 151.89 million clean reads were generated. All reads were assembled into 57,077 unigenes, and 24,574 could be annotated. By comparing the gonad transcriptomes, 11,487 differentially expressed genes were obtained, of which 4599 were upregulated and 6888 were downregulated in the ovaries. Using enrichment analyses, many functional pathways were found to be associated with reproduction regulation. A set of sex-biased genes putatively involved in gonad development and gametogenesis were identified and their sexually dimorphic expression patterns were characterized. The detailed transcriptomic data provide a useful resource for further research on <i>D. hystrix</i> reproductive manipulation.
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