Phialocephala was established for species in the Leptographium complex that produce conidia from phialides at the apices of dark mononematous conidiophores. Some species previously included in Phialocephala were re-allocated to Sporendocladia because they resembled Thielaviopsis in having ring-wall-building conidial development and conidia with two attachment points that emerge in false chains. Despite this significant realignment of the genus, a great deal of morphological heterogeneity remains in Phialocephala. The objective of this study was to consider the heterogeneity among Phialocephala spp. based on comparisons of sequence data derived from the large and small subunits (LSU and SSU) of the rRNA operon of species in Phialocephala. Phialocephala dimorphospora, the type species of the genus, and P. fortinii grouped with genera of the Helotiales in phylogenetic trees generated based on the LSU and SSU datasets. Phialocephala xalapensis and P. fusca clearly are unrelated to Phialocephala sensu stricto and should represent a new genus in the Ophiostomatales. Phialocephala compacta resides with representatives of the Hypocreales, and we believe that it represents a distinct genus. Phialocephala scopiformis and P. repens are not closely related to the other Phialocephala species and group within the Dothideales. The morphological heterogeneity among species of Phialocephala clearly is reflected by phylogenetic analysis of sequence data from two conserved rRNA gene regions. Appropriate genera now need to be found to accommodate these fungi.