The Peltigera didactyla complex comprises species of section Peltigera with laminal and submarginal soredia. Three species (P. didactyla, P. lambinonii, and P. ulcerata) and one atypical variety (P. didactyla var. extenuata) are currently recognized within this complex. Phylogenetic inferences of the entire Internal Transcribed Spacer region (ITS) and the 5′ half of the gene encoding the large subunit of the rRNA reveal a robust structure within the complex. Under both the maximum parsimony and the maximum likelihood criterion, P. didactyla is resolved as a polyphyletic entity, whereas P. ulcerata, P. lambinonii, and P. didactyla var. extenuata are delimited as monophyletic entities. Peltigera didactyla var. extenuata appears basal within the group, whereas var. didactyla is nested within a clade that also comprises P. lambinonii and P. ulcerata. The polyphyly of P. didactyla is further characterized by the existence of populations that resemble var. extenuata, but differ by their brownish upper cortex. These populations, all from the boreal zone of Canada, compose a monophyletic group sister to the P. didactyla-P. lambinonii clade. For P. didactyla to satisfy a phylogenetic species concept, the var. extenuata is reinstated at the species level, and a new species, P. castanea, is described. Three populations sampled are characterized by unique sequences that may indicate the presence of additional cryptic taxa within the complex. A key to the accepted species is provided. The presence of P. lambinonii in Australia is confirmed and P. ulcerata is reported as new for Chile.