Autophagy is a major cellular degradation pathway in which materials are delivered to the vacuole in double-membrane vesicles known as autophagosomes, broken down, and recycled (Li and Vierstra, 2012; Liu and Bassham, 2012). In photosynthetic organisms, the pathway is strongly activated by biotic and abiotic stresses, including nutrient limitation, oxidative, salt and drought stress and pathogen infection, and during senescence (Perez-Perez et al., 2012; Lv et al., 2014). Mutation of genes required for autophagy causes hypersensitivity to stress, indicating that autophagy is important for tolerance of multiple stresses. While autophagy is often non-selective, a growing number of examples of selectivity are now evident, in which specific cargos are recruited into autophagosomes via cargo receptors (Floyd et al., 2012; Li and Vierstra, 2012). In this Research Topic, a series of original research articles and reviews highlight areas of current focus in plant and algal autophagy research, including mechanisms and cargos of selective autophagy, lipid degradation, and metabolic and physiological consequences of the autophagy pathway.