Abstract: Sea urchin（Strongylocentrotus intermedius） is an important mariculture species, and gonads are the only edible part in sea urchins. The sea urchin industry exhibits highly seasonal characteristics, thus realization of artificial control of its sexual maturity will be of great economically value. Using a high-throughput sequencing technology, we performed full-length transcriptome sequencing on the gonads of females and males, sampled in the nutritive phagocyte（NP） recovery phase of gonadal development in S. intermedius to identify genes related to gonadal development. By de novo assembly, 64 949 unigenes were obtained, and a total of 23 848（36.72%） functional genes were annotated by homology matching analysis. Then 15 985 differentially expressed genes（DEGs） were identified by comparing the expression levels of these unigenes between testes and ovaries. Compared with testes, 8 355 were up-regulated and 7 630 were down-regulated in ovaries. By using GO clustering analysis and differential gene expression analysis, we obtained 14 testes specifically expressed genes（DMRT1, Catspere, Meioc, etc.）, and 16 ovaries specifically expressed genes（TGFBI, EGF3, EGF1, etc.）, and 19 evolutionarily conserved sex-related genes（Spata4, DMC1, HSF5, gata4, etc.）, This study provides foundation for studying the gonadal development mechanism of S. intermedius.