This species has something of a confused history having been previously been considered synonymous with both A. sophiae and A. fasciatus. Another species, A. chantrei is still listed as valid by some sources but is now known to be a junior synonym of A. danfordii. This became clear during a 1999 study in which the type specimens of A. danfordii were found to be indistinguishable from the Aphanius population living in the Sultan Swamps, the type locality of A. chantrei.

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