Chaenotheca Th. Fr. is associated with four different genera of photobionts, Dictyochloropsis, Stichococcus, Trebouxia, and Trentepohlia. The species of Chaenotheca consistently harbor only one photobiont genus. A molecular phylogeny based on their ITS1-5.8-ITS2 sequences of 16 species is presented. It contains five well supported clades. In two clades the species were only associated with Stichococcus, and one only with Trebouxia. In the other two clades two or three photobiont genera were present. Thus there is a partial congruence between photobiont association and cladogenesis in the genus. Section Cystophora, characterized by its association with Trebouxia, and sect. Allodium, with Stichococcus, are polyphyletic in the molecular phylogeny. The subgenera Chaenotheca and Cystophora are characterized by ascus shape and secondary chemistry. Two distinctive clades in the molecular phylogeny contain species referred to subg. Chaenotheca and two other distinctive clades contain species referred to subg. Cystophora. However, one of the two clades containing species of subg. Chaenotheca has a clade of species belonging to subg. Cystophora as sister group, and the other one has all the other species as sister group. These relationships, although only have weak support.