Autophagy is an evolutionarily conserved lysosome-based degradation process. Atg5 plays a very important role in autophagosome formation. Here we show that Atg5 is required for biogenesis of late endosomes and lysosomes in an autophagy-independent manner. In Atg5 (-/-) cells, but not in other essential autophagy genes defecting cells, recycling and retrieval of late endosomal components from hybrid organelles are impaired, causing persistent hybrid organelles and defective formation of late endosomes and lysosomes. Defective retrieval of late endosomal components from hybrid organelles resulting from impaired recruitment of a component of V1-ATPase to acidic organelles blocks the pH-dependent retrieval of late endosomal components from hybrid organelles. Lowering the intracellular pH restores late endosome/lysosome biogenesis in Atg5 (-/-) cells. Our data demonstrate an unexpected role of Atg5 and shed new light on late endosome and lysosome biogenesis.