The classification of Jakoba is debated.

Patterson (1990) created the new family Jakobidae for the genus, but chose not to assign the family to any larger group. He reasoned that too little was known about the genus, and about small heterotrophic flagellates in general, to permit any assignment except on the basis of guesswork.

If the "jakobid hypothesis" is correct (see Introduction), then Jakoba is one of the most ancient of the eukaryotes in the lineages with tubular and flattened mitochondrial cristae. This phylogenetic position would then be reflected in its classification.

Cavalier-Smith (1993) proposed a full hierarchical classification for Jakoba:

This classification, which remains controversial, separates Jakoba and the histionids (Histiona and Reclinomonas) at the level of subphylum, which is difficult to reconcile with the close similarities among these "jakobid" protists in ultrastructural and mitochondrial genome features.

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