Hydrogenosomes, membrane-bounded organelles that compartmentalize the terminal reactions of cellular energy metabolism, were first described in the parabasalid flagellate Tritrichomonas foetus as subcellular compartments that produce hydrogen and ATP (adenosine triphosphate). Since then, these organelles have been described in a number of different unicellular eukaryotes adapted to microaerobic or anoxic environments. Recent studies have led researchers to consider hydrogenosomes as variations of mitochondria adapted to anaerobic environments, a concept that is supported by the finding of rudimentary mitochondrial-remnant organelles in organisms previously considered devoid of energy-generating organelles (the Archezoa). The relationship of these energy-generating organelles to each other and to the mitochondrion has been examined by many researchers, and several theories have been put forward to explain their origins. In this article, we hope to correct some misconceptions concerning the relationships of the hydrogenosomes so far described, and to put forward an argument that supports the concept that hydrogenosomes evolved repeatedly, either from a protomitochondrion or from differentiated mitochondria.