Endocytosis plays an important role in plant physiology, but how endocytic organelles are organized remains unknown. We present the evidence that endosomes are functionally differentiated in Arabidopsis cells. Two types of Rab5-related GTPases are localized on distinct population of endosomes in a partially overlapping manner. Ara7 and Rha1 are on an early type of endosomes with AtVamp727, where recycling of plasma membrane proteins occurs. In contrast, the plant-unique Rab5, Ara6, resides on distinct endosomes with the prevacuolar SNAREs. Partially overlapping localization of Ara6 and Ara7/Rha1 with reciprocal gradients suggests maturation of endosomes from one to the other.