Phagocytosis of apoptotic cells and cellular debris is a critical process of maintaining tissue and immune homeostasis. Defects in the phagocytosis process cause autoimmunity and degenerative diseases. Phagocytosis ligands or “eat‐me” signals control the initiation of the process by linking apoptotic cells to receptors on phagocyte surface and triggering signaling cascades for cargo engulfment. Eat‐me signals are traditionally identified on a case‐by‐case basis with challenges, and the identification of their cognate receptors is equally daunting. Here, we identified galectin‐3 (Gal‐3) as a new MerTK ligand by an advanced dual functional cloning strategy, in which phagocytosis‐based functional cloning is combined with receptor‐based affinity cloning to directly identify receptor‐specific eat‐me signal. Gal‐3 interaction with MerTK was independently verified by co‐immunoprecipitation. Functional analyses showed that Gal‐3 stimulated the phagocytosis of apoptotic cells and cellular debris by macrophages and retinal pigment epithelial cells with MerTK activation and autophosphorylation. The Gal‐3‐mediated phagocytosis was blocked by excessive soluble MerTK extracellular domain and lactose. These results suggest that Gal‐3 is a legitimate MerTK‐specific eat‐me signal. The strategy of dual functional cloning with applicability to other phagocytic receptors will facilitate unbiased identification of their unknown ligands and improve our capacity for therapeutic modulation of phagocytic activity and innate immune response. J. Cell. Physiol. 227: 401–407, 2012. © 2011 Wiley Periodicals, Inc.