GABA(subB) receptors are heterodimeric G protein-coupled receptors that mediate slow synaptic inhibition in the CNS. While heterodimerization between GABA(subB) receptor GABA(subB)R1 and GABA(subB)R2 subunits is essential for functional expression, how neurons coordinate the assembly of these critical receptors remains to be established. Here we have identified Marlin-1, a novel GABA(subB) receptor binding protein that associates specifically with the GABA(subB)R1 subunit in yeast, tissue culture cells and neurons. Marlin-1 is expressed in the brain and exhibits a granular distribution in cultured hippocampal neurons. Marlin-1 binds different RNA species including the 3 untranslated regions of both the GABA(subB)R1 and GABA(subB)R2 mRNAs in vitro and also associates with RNA in cultured neurons. Inhibition of Marlin-1 expression via sRNAi technology results in enhanced intracellular levels of the GABA(subB)R2 receptor subunit, without affecting the level of GABA(subB)R1. Together our results suggest that Marlin-1 functions to regulate the cellular levels of GABA(subB) R2 subunits, which may have significant effects on the production of functional GABA(subB) receptor heterodimers. Therefore, our observations provide an added level of regulation for the control of GABA(subB) receptor expression and for the efficacy of inhibitory synaptic transmission.