Autophagy is a self-protective mechanism that degrades inner and outer invaded substances to sustain self-maintenance. SNARE (Soluble N-ethylmaleimide-sensitive factor attachment protein receptors) hypothesis suggests important roles of SNARE proteins in the cellular activities of substance transport and specific membrane fusion, unveiling the molecular mechanisms of normal and physiological activities within a cell. Since autophagy involves membrane fusions from the birth of autophagosomes to the formation of autolysosomes, we review recent research progress on the roles of SNARE proteins in regulating autophagy.