Our understanding of the microcell oyster parasites of the genera Bonamia and Mikrocytos has expanded in recent years with the application of ultrastructural and especially molecular biological research approaches. Molecular phylogenetic analyses of SSU rRNA genes have united three species, Bonamia ostreae, Bonamia exitiosa, and Mikrocytos (now Bonamia) roughleyi, in a microcell clade within the Haplosporidia, supporting both early and recent ultrastructural observations. Ultrastructural and molecular phylogenetic evidence has emerged that Mikrocytos mackini, on the other hand, is a unique protist with unusual adaptations for a parasitic existence. DNA probes and polymerase chain reaction (PCR) assays promise new insights into the life cycles, transmission, and diversity of these organisms. The development of Ostrea edulis lines selected for B. ostreae resistance will increase the viability of aquaculture industries for this species and, combined with rapidly developing biotechnological approaches for studying host defenses and host-parasite interactions, will allow greater insight into the nature of phenomena such as resistance and tolerance to disease in oysters.