Jakobid flagellates are small, free-living, bacterivorous heterotrophs, with similar morphology, asexual reproduction, and nucleocytoplasmic ultrastructural features at interphase and during cell division. Jakoba is typified by aloricate trophic cells, each containing a branched mitochondrion with prominent nucleoids and flattened cristae. Reclinomonas and Histiona are characterized by loricate trophic cells, each with an unbranched mitochondrion without prominent nucleoids or otherwise differentiated regions and bearing tubular cristae. An undescribed genus is typified by aloricate cells, each with an unbranched mitochondrion bearing discoidal cristae. I propose, on the basis of cytoskeletal architecture and other structural and developmental features, that jakobids are ancestral mitochondrial protists, sister taxa to the amitochondrial retortamonads and ancestral to diverse lineages of mitochondrial eukaryotes. Application of different classification paradigms produces different family-level taxonomies for jakobids.