So far, the genus Jakoba has only the one species, J. libera.

Until 1990, this species was known as Cryptobia libera Ruinen, 1938. Ruinen thought she had found a free-living member of the trypanosomatid genus Cryptobia, otherwise known only as parasitic protists. Hence, the species epithet (libera in Latin means "free", "at liberty"). Studies on the protist's ultrastructure and the molecular biology of its mitochondrial genome have demonstrated that it is not a member of the trypanosome group. The genus name was changed to reflect this change in scientific perception of the phylogenetic position of the organism.

The genus is named after the discoverer of its only species, Dr. Jakoba Ruinen.

For lookalike taxa see Similar genera.

For issues associated with the higher-level classification of Jakoba, see Classification.

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