During a survey of the lichen flora of the Darel Valley in Gilgit Baltistan and the Sharan Valley in Khyber Pakhtunkhwa many lichen specimens were collected. These specimens were analyzed using morpho-anatomical, molecular, and chemical test methods. Two species new to Pakistan, Lecidella flavosorediata and Pertusaria qilianensis, and one new to Gilgit Baltistan, Verrucaria nigrescens were discovered in the collection. Phylogeny, distribution, ecology, and morpho-anatomical descriptions of the species are given. Keywords: Darel, Lecanoraceae, Phylogeny, Pertusariaceae, Sharan, Verrucariaceae.