A new combination was proposed by Johnson and collaborators in 2005 transferring Achlya hypogyna to the genus Protoachlya based on morphological evidence. However, the proposed name Protoachlya hypogyna was not legitimate because it had been already adopted for another species. Therefore, a new name for this taxon is herein proposed and morphological and phylogenetic analyses are presented justifying the position of this species inside the genus Protoachlya. For the first time, ITS and LSU sequences of P. hypogyna are used in a phylogenetic analysis and deposited in GenBank.