The first molecular phylogenetic study on a range of Punctelia species is reported, focussing on specimens growing in the Iberian Peninsula. Material of seven species was included in the analysis. Forty sequences were generated from nuITS and mtSSU rDNA in 20 specimens, and the resultant majority rule consensus tree from the combined analyses shows four major clades. Punctelia ulophylla is confirmed as a distinct species, P. reddenda is basal to P. borreri, and P. perreticulata groups with P. subrudecta. Samples identified as P. rudecta from the Canary Islands and China occupy different basal positions; the complex merits further study. Punctelia borreri and P. subrudecta are mainly coastal in the Iberian Peninsula, but are now reported from the central plateau for the first time; newly colonizing thalli have been found in a park in Madrid which is regularly spray-watered and where sulphur dioxide levels have fallen over the last two decades.