The fate and function of mitochondria and peroxisomes are tightly coupled. Their biogenesis is linked through common transcriptional pathways, and their growth and division is mediated by common fission machinery. Recently, these two organelles have been linked in a much more direct manner, where mitochondrial derived vesicles deliver specific cargo into a population of peroxisomes. There are a number of concepts that emerge from this observation, including the idea that mitochondria are able to segregate their contents into vesicles and that vesicles may represent a new mechanism for mitochondrial communication with peroxisomes, and potentially other intracellular organelles. By considering the function of their bacterial relatives, we can develop hypothesis about the origin and mechanism of mitochondrial vesicle formation. The vesicles released from bacteria have numerous functions in signaling within the colony and mediating host infection. Therefore, the first observation that the mitochondria form vesicles that are transported within the cell defines a new, evolutionarily conserved process in mitochondrial cell biology and dynamics. This review will explore the mechanism and function of mitochondrial vesicle transport with an eye toward the evolutionary implications of this new pathway in cell biology.