The genus Paraphaeosphaeria (Loculoascomycetes) was described as a segregate of Leptosphaeria for species producing brown, usually punctate ascospores with rounded ends, a submedian primary septum, an inflated cell above the primary septum, and a Coniothyrium sensu lato anamorph. This study evaluated the taxonomic value of the morphological characters, host range, ecology, and anamorphs in relation to DNA sequence data in order to determine the relationship between species described in Paraphaeosphaeria. Nine species were characterized morphologically and the ITS and 18S regions of the rDNA were sequenced and a phylogeny was inferred. Morphological studies and results of the sequence analyses provide strong support for polyphyly of this genus. Based on these analyses, the concept of Paraphaeosphaeria should be narrowed to reflect a monophyletic generic concept. Characters such as spore septation and method of conidiogenesis were found to predict relatedness.