The interphotoreceptor matrix (IPM) is a specialized extracellular mesh of molecules surrounding the inner and outer segments of the photoreceptor neurons. The interphotoreceptor matrix proteoglycan 1 and 2 (IMPG1 and IMPG2) are major components of the IPM. Both proteoglycans possess SEA (Sperm protein, Enterokinase and Agrin) domains, which are described to support protein proteolysis. Interestingly, humans with mutations in the SEA domains of IMPG1 and IMPG2 are associated with retinitis pigmentosa (RP) vision disease. This work investigates the SEA-mediated proteolysis of IMPG1 and IMPG2 and its significance to IPM physiology. Western blot relative molecular mobility analysis of IMPG1 from retina confirmed protein proteolysis. Point mutations in the SEA domain of IMPG1 inhibit protein proteolysis, as shown in cell culture assays. Likewise, IMPG2 also proteolyzes at the SEA domain generating two subunits: a membrane-attached and an extracellular peptide, as seen by western blot and immunohistochemical assays. Importantly, the extracellular portion of IMPG2 traffics toward the outer segment IPM by a mechanism dependent on IMPG1. These results demonstrate that proteolysis is part of the maturation of IMPG1 and IMPG2, which is important for protein localization and linked to vision diseases. Moreover, the results indicate interdependency between IMPG1 and IMPG2, which helps understand the molecular mechanisms involved in the development of vision diseases in patients with defective IMPG molecules.