To explore the functions of long non-coding RNA in the differentiation of gonads, we performed next-generation sequencing on strand-specific RNA libraries where rRNA was depleted from total RNA extracted from three testes and three ovaries of the large yellow croaker (). In total, 66088 transcripts derived from 31675 genes were obtained from the sequencing data of the large yellow croaker; 5162 lncRNAs from 3984 gene loci were retained after stringent filtering. There were 9341 differentially expressed mRNAs and 2782 lncRNAs between the male and female gonads at the gene level. Furthermore, Pearson correlation coefficients were calculated between the differentially expressed lncRNAs and their adjacent genes using the expression data. We detected 1227 highly correlated lncRNA-mRNA pairs, among which, multiple lncRNAs targeted genes related to sex differentiation. lncRNA MSTRG.24346 was close to (<17 kb) and highly significantly correlated with the sex-differentiation candidate gene in the large yellow croaker. Thus, this study showed that lncRNA may play important roles in the sex differentiation of the large yellow croaker.