Rbmy gene encodes a RNA-binding protein and its expression is limited to the nuclei of germ cells. Previous studies indicate that RBMY may function in pre-mRNA processing during spermatogenesis, although its precise target mRNAs remain unclear. By using specific nucleic acids associated with proteins and immunoprecipitation techniques, we have identified 12 potential target mRNAs bound by mouse RBMY protein from testis. We detect that both mRbmy-1 and mRbmy-2 transcripts co-exist in mouse testis and they differ mainly in the 5′UTR. Importantly, our result shows that mRBMY protein can bind to one of its own transcripts, mRbmy-2, suggesting that mRBMY may affect alternative splicing or regulate the expression of its own gene. Using electrophoretic mobility shift assay, we demonstrated that mRBMY protein can bind to the testis and sperm-specific spa17 mRNA and that the binding domain contains rich oligo(A), suggesting that mRBMY protein may have high affinity to oligo(A) rich sequences. In conclusion, the identification of RBMY target mRNAs will be helpful to further explore the biological function of RBMY in spermatogenesis.