We identified eight genes of putative RGS proteins in skin of Medaka fish using PCR amplification with degenerate primers for the RGS domain of known RGS proteins. Then, we cloned a full-length cDNA for a new RGS protein. This RGS protein was similar to human RGS3 within the RGS domain, but other parts were unique among known RGS proteins. RT-PCR analysis demonstrated that this Medaka RGS3-like protein (MeRGS3L) is mainly expressed in skin and heart. When coexpressed in Xenopus oocytes, MeRGS3L accelerated the turning-on and -off of Gi/o-mediated modulation of GIRK channels without apparent desensitization in the presence of ligand. MeRGS3L also decreased the response of Gq signaling upon activation of m1 muscarinic receptor. This new RGS protein may play important roles in regulation of melanophore responses in Medaka skin.