The best studied hydrogenosomes are those of the sexually transmitted parasites Trichomonas vaginalis and Tritrichomonas foetus and those from rumen chytrids such as Neocallimastix.
The anaerobic ciliated protozoan Nyctotherus ovalis, found in the hindgut of several species of cockroach, has numerous hydrogenosomes that are intimately associated with endosymbiotic methane-producing archaea, the latter using the hydrogen produced by the hydrogenosomes.