Jaapia is a wood-saprobic genus of corticioid fungi for which two species have been recognized: J. argillacea Bres. and J. ochroleuca (Bres.) Nannf. & J. Erikss. Whereas the first one is easily recognized by its characteristic spores, the descriptions of the second indicated variable spores, which once led us to believe that J. ochroleuca could be a species complex rather than a single species. Eleven new ITS nrDNA sequences of J. ochroleuca were aligned with two obtained from GenBank and four of J. argillacea. The molecular results, parsimony analysis and KP2 distances clearly delimitate one highly supported Jaapia clade, with two subclades that correspond to the two described species. Morphological studies, including the holotype and isotype of J. ochroleuca, show significant differences between the clades concerning the size and shape of spores. The present study corroborates two species in this genus and also confirms that J. ochroleuca is a well-defined species in which spores show great morphological variability. Based on the Jaapia “species hypothesis”, the J. ochroleuca reference sequence has been selected. A comprehensive key to two Jaapia species is also provided.