The sunbittern is usually placed in the Gruiformes, but this was always considered preliminary. Altogether, the bird is most similar to another bird that was provisionally placed in the Gruiformes, the kagu (Rhynochetos jubatus). Molecular studies seem to confirm that the kagu and sunbittern are each other's closest living relatives and have a similar wing display. They are probably not Gruiformes (though the proposed Metaves are just as weakly supported). Altogether, the two species seem to form a minor Gondwanan lineage which could also include the extinct adzebills and/or the mesites, and is of unclear relation to the Gruiformes proper. Notably, the kagu and mesites also have powder down.
The sunbittern was formerly treated as two species (E. helias and E. major), but now they are treated as a single species with considerable variation between the subspecies. The three subspecies are recognised on the basis of plumage characters and size. The three subspecies are allopatric.
- E. h. helias (Pallas, 1781) – Amazonian sunbittern
- E. h. major Hartlaub, 1844 – northern sunbittern
- E. h. meridionalis Berlepsch & Stolzmann, 1902 – foothill sunbittern