Rbmy gene encodes a germ-cell specific nuclear RNA-binding protein and is involved in spermatogenesis. To further investigate the specific events of spermatogenesis in which Rbmy plays a role, the target mRNAs of human RBMY protein were isolated and identified. Through the isolating specific nucleic acids associated with proteins (SNAAP) technique, we isolated twenty potential target genes of human RBMY protein from the human testis in the present study. Some of these target genes play important roles during spermatogenesis and have alternative transcripts in the testis. In this study, we focused on the human- related (never in mitosis gene a) kinase 10 (Nek10) gene, which belongs to the Nek protein kinase subfamily. Nek10 has two transcripts, and the results of RT-PCR and Electrophoretic Mobility Shift Assays (EMSA) show that hRBMY protein can only bind to transcript variant 2 of Nek10 and that hRbmy may take part in alternative splicing of Nek10. Isolation and identification of target genes of hRBMY will be helpful to further investigate the biological function of RBMY in spermatogenesis.