For this study, a number of species of the genus Cladonia were collected from different areas of Pakistan and characterized using morpho-anatomical and molecular techniques. The present work revealed that the collected specimens belong to four species. Among these, C. rei, C. ochrochlora and C. cariosa are new records for Pakistan, while the reports of C. pocillum represent range extensions within Pakistan. Complete morpho-anatomical descriptions and notes on ecology and distribution are provided, along with ITS-based molecular analysis. Keywords: Cladoniaceae; lichen-forming fungi; macrolichens; Muzaffarbad; phenotypic; Swat.