Spilonema was originally described to accommodate an unusual group of cyanolichens with thread-like, cushion-forming thalli, and has long been placed in Coccocarpiaceae based on ascomatal development. However, Spilonema is the only genus of Peltigerales to include species lichenized with the cyanobacterial genus Stigonema, and the evolutionary relationships of Spilonema to other genera in the family have yet to be tested using molecular data. We present evidence from combined nuclear 28S, 18S and mitochondrial 12S rDNA to confirm the placement of the core species of Spilonema (S. paradoxum and S. revertens) in Coccocarpiaceae. Our data further show that despite possessing a different genus of photobiont (Scytonema), the north Pacific endemic genus Spilonemella must be included within Spilonema, suggesting that closely related species of the genus have changed photobionts in the course of evolution. However, we recovered Spilonema dendroides, one of the only lichens known to associate with the cyanobacterial genus Hyphomorpha, as only distantly related to the Coccocarpiaceae. The evolutionary relationships of this species are as yet unclear but it may occupy a basal position in the Peltigerales. We create for this species the new genus Erinacellus T. Sprib., Muggia & Tønsberg.