Newly designed algal-specific primers were used to amplify the ribosomal ITS region from 25 photobiont specimens from five lichenized fungi of the family Physciaceae (Lecanorales), Anaptychia ciliaris, Phaeophyscia orbicularis, Physcia caesia, P. tenella, and Physconia distorta. The obtained DNA sequences were then phylogenetically analyzed using parsimony jackknifing. The analyses indicated that the mycobionts associated with two photobiont species: Trebouxia impressa was found with all mycobionts, except Anaptychia ciliaris, which instead was associated with Trebouxia arboricola. In the jackknife tree, all Trebouxia arboricola sequences formed a monophyletic group with a high jackknife support. The Trebouxia impressa sequences also formed a well supported group, which in turn had some internal structure. The photobiont species is reported for the first time for Anaptychia ciliaris, Physcia caesia, and P. tenella. A phylogenetic tree for the photobiont, T. impressa, was compared to a phylogeny of the corresponding mycobionts, also based on ITS sequences. A combined analysis of the data from the photobiont and the data from the mycobiont was also performed. Several similarities were found in the tree topologies. The general similarity of the mycobiont and photobiont trees may indicate a coevolutionary history.