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Lichen of the genus Usnea are used as a traditional herbal remedies. This genus has the thallus which is very similar among species, so it is very difficult to distinguish. Based on morphological character, identification of species in Indonesia is still limited. Morphological characters is can be used to identify in family and genus only. The molecular character based on DNA Barcode of Internal Transcribed Spacer (ITS) rDNA sequences which has conserved region (5.8S) and varied region (ITS1 and ITS2) is needed to strengthen and support the identification and phylogenetic analysis. The objective of this research was to identify and make phylogenetic analysis of Usnea species from the forest of Gunung Lawu, Center Java and Turgo, Yogyakarta. Phylogenetic tree was constructed with Maximum Likelihood (ML), the model of evolution Kimura-2 parameter with the bootstrap 1000. The result of phylogenetic tree reconstruction show within main two clades, section Usnea and Eumitria in the genus Usnea. The ITS rDNA sequence was able to identify most of the Usnea, but do not support the separation of the lichens Usnea pectinata and Usnea baileyi as distinct species.