Mutations in the human Crumbs homologue 1 (CRB1) gene are a frequent cause of various forms of retinitis pigmentosa. The CRB1-membrane-associated palmitoylated protein (MPP)5 protein complex is thought to organize an intracellular protein scaffold in the retina that is involved in maintenance of photoreceptor-Müller glia cell adhesion. This study focused on the binding characteristics and subcellular localization of MPP3, a novel member of the MPP5 protein scaffold at the outer limiting membrane (OLM), and of the DLG1 protein scaffold at the outer plexiform layer of the retina. MPP3 localized at the photoreceptor synapse and at the subapical region adjacent to adherens junctions at the OLM. Localization studies in human retinae revealed that MPP3 colocalized with MPP5 and CRB1 at the subapical region. MPP3 and MPP4 colocalized with DLG1 at the outer plexiform layer. Mouse Dlg1 formed separate complexes with Mpp3 and Mpp4 in vivo. These data implicate a role for MPP3 in photoreceptor polarity and, by association with MPP5, pinpoint MPP3 as a functional candidate gene for inherited retinopathies. The separate Mpp3/Dlg1 and Mpp4/Dlg1 complexes at the outer plexiform layer point towards additional yet unrecognized functions of these membrane associated guanylate kinase proteins.