Informal ascomycete classifications have traditionally been based in part on ascomatal morphologies. The problems associated with grouping taxa using ascomatal characters are evidenced in the Coccotremataceae where the ascomata have been interpreted either as apothecia or perithecia. We used SSU rDNA sequences representing all classes of the Pezizomycotina to infer the phylogenetic position of the family. The Coccotremataceae clustered within the Lecanoromycetes. Since the Lecanoromycetes are characterized by the presence of apothecia, these data support the apothecial interpretation, given that the ascomata of the Coccotremataceae are not the result of convergent evolution. To evaluate the ordinal placement of the Coccotremataceae we used sequences of the SSU rRNA and LSU rRNA gene of 12 Lecanoromycetes. The SSU and LSU portions of this second analysis reveal conflicting phylogenies. Therefore we compared the two portions with additional statistical tests: splits decomposition, an analysis of the distribution of homoplasy, and a calculation of the ideal nucleotide substitution rate. In all of these tests the LSU data performed better than the SSU data. The results of the incongruence length difference (ILD) test suggest the data portions could be combined. There is no difference in the tree topology of the combined data set and of the LSU portion only, but the bootstrap values in the combined tree are lower. We argue that the low bootstrap supports in the combined tree are due to the phylogenetic signal in the SSU data set. Therefore we use the LSU and the combined tree to base our classification of the Coccotremataceae. In the LSU and the combined tree the inclusion of the Coccotremataceae in the Pertusariales is supported as is the sister relationship of the Pertusariales and Agyriales. Within the Pertusariales the Coccotremataceae and Pertusariaceae are well-supported sister taxa.