Recent finds of Leightoniella zeylanensis, classified variously in the Collemataceae and Pannariaceae, enabled us to generate DNA sequence data for investigating its phylogenetic affiliation. Newly generated sequence data from the internal transcribed spacer (ITS) region and the large subunit of the nuclear ribosomal DNA (nrLSU), the small subunit of the mitochondrial ribosomal (mrSSU) DNA, and the largest subunit of the RNA polymerase II gene (RPB1) indicate that L. zeylanensis is a member of the Pannariaceae, belonging to a strongly supported clade together with Physma, Lepidocollema, and Gibbosporina (= the ‘Physma clade’). With the currently available data, however, relationships within this clade are largely impossible to reconstruct with confidence. Leightoniella zeylanensis was found to possess ellipsoid ascospores surrounded by a thick, gelatinous perispore with pointed ends, supporting a previously published hypothesis that such a perispore type is a synapomorphy for the Physma clade. A lectotype is designated for the basionym Pterygium zeylanense Leight.