Abstract Microbodies in six anaerobic ciliated protozoa (Metopus, Brachonella, Plagiopyla, Parablepharisma, Sonderia, Saprodinium) were found to be enclosed by two membranes. The inner membrane showed extensive infolding, division stages were observed, and in all genera apart from Sonderia and Parablepharisma, the microbodies contained an hydrogenase and were attached to methanogenic bacteria. Some of these ciliates are related to aerobic species with mitochondria. We believe that the microbodies are hydrogenosomes, that they are derived from mitochondria, and that their biochemical modification has incurred little change in the original mitochondrial ultrastructure. These observations weaken the case for the independent origin of hydrogenosomes from anaerobic prokaryotes.