The ubiquitin/proteasome pathway plays an important role in gametogenesis. Ubiquitin/ribosomal fusion protein is the precursor of mono-ubiquitin. We identified two ubiquitin/ribosomal fusion proteins genes in testis of Eriocheir sinensis. The ubiquitin-ribosomal proteins S27 and L40 are denoted as UBS27 and UBL40, respectively. The full length Es-UBS27 cDNA (565 bp) was cloned using PCR, based upon an initial expressed sequence tag (EST) isolated from a testicular cDNA library and the result of 3′ RACE. The sequence contained a 465-nucleotide open reading frame (ORF) that encoded a protein of 154 amino acids. It contained a Ubiquitin (UB) domain and the ribosomal protein S27. The full-length Es-UBL40 cDNA (521 bp) contained a 390-nucleotide ORF that encoded a protein of 129 amino acids. It contained a UB domain and the ribosomal protein L40. By real-time PCR, the expression level of these two UB genes is shown to change significantly in the developing testis and ovary, reaching peak expression in August and October, respectively. During accessory gonad seasonal development, the expression of UBS27 and UBL40 varied sharply and reached peak expression in November. In situ hybridization of testis and ovary, indicated that UB transcription took place widely. Our study demonstrates, for the first time, that UBS27 and UBL40 play key roles in gametogenesis and reproductive success in Eriocheir sinensis.