The toad was formerly considered part of the Atelopus spumarius. It is not clear whether or not it is a single species or a group of related species. In the past the species has also been called Atelopus flavescens.^[1]

Several publications have touched on the subject of Atelopus barbotini. In 2005 Noonan and Gaucher wrote in Molecular Ecology that there was evidence that Atelopus barbotini might not be conspecific with Atelopus spumarius. They didn't make a change to the taxology of the species though. In 2011 Lötters, van der Meijden, et al. argued that Atelopus barbotini and Atelopus spumarius were not conspecific, but that Atelopus flavescens may be conspecific with Atelopus barbotini.

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