The occurrence of 12 Usnea species in Estonia is verified by investigating c. 1800 specimens. The known distribution and substratum preferences of Usnea taxa in Estonia are summarized. Picea is the main substratum for Usnea species in Estonia, but occasionally these species occur also on deciduous trees, wood, and exceptionally on rock. A key for identification of 16 taxa recorded in the three Baltic countries is provided and diagnostic morphological and chemical characters used in the key are discussed. A new chemotype of U. fulvoreagens has been identified. U. wasmuthii is reported as new to Lithuania.