At present, Malawimonas jakobiformis is known from one clonal strain. Apart from jakobids, which differ from Malawimonas in e.g. kinetid architecture, Golgi morphology, structure of extrusome-like organelles, and shape of mitochondrial cristae, Malawimonas has no close relatives. Further resolution of the taxonomy and classification of the species awaits further discoveries of protists with jakobid affinities.
For lookalike taxa see Similar genera.
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