While misfolded and short-lived proteins are degraded in proteasomes located in the nucleus and cytoplasm, the degradation of organelles and long-lived proteins in the lysosome occurs by the process of autophagy. Central and necessary to the autophagic process are two conserved ubiquitin-like conjugation machineries. These conjugation machineries appear to be specific for autophagy and can together with genetic and morphological data be used to trace the natural history of autophagy. Here we discuss the origin and evolution of autophagy.