Amur catfish is extensively distributed and cultured in Asian countries. Despite of economic importance, the genomic information of this species remains limited. A reference transcriptome of Amur catfish was assembled and the sex-biased gene expression in the gonads was characterized using RNA-sequencing. The assembled transcriptome of Amur catfish consisted of 74,840 transcripts. The N50, mean length and max length of transcripts are 1970, 1235 and 16,748 bp. Putative sex-specific transcripts were identified and sex-specific expression of the representative genes was verified by RT-PCR. Differential expression analysis identified 5401 ovarybiased and 5618 testis-biased genes. The ovary-biased genes were mainly enriched in pathways such as RNA transport and ribosome biogenesis in eukaryotes. The testis-biased genes were enriched in calcium signaling and cytokine-cytokine receptor interaction, etc. Our data provide a valuable genomic resource for further investigating the genetic basis of sex determination, sex differentiation and sexual dimorphism of catfish.