Two new Pertusaria species with brown ascospores are described from southern California and Baja California, Mexico. Pertusaria islandica sp. nov. is characterized by pertusariate to pseudolecanorate ascomata, ellipsoid ascospores, 8-spored asci, a strongly K+ violet reacting epithecium, and the presence of the 2′-O-methylperlatolic acid chemosyndrome, while P. occidentalis sp. nov. has pertusariate ascomata, globose to subglobose ascospores, 8-spored asci, and contains the arthothelin chemosyndrome. Pertusaria ochracea Kremp. is reduced to synonymy with P. melanospora Nyl.