The variability of the composition of secondary metabolites in Hypogymnia vittata and H. subduplicata was studied. Three chemotypes have been identified for H. vittata differing in the composition of the orcinol depsidones of the medulla: I — contains vittatolic acid, 3-hydroxyphysodic and physodic acids; II — contains 3-hydroxyphysodic and physodic acids; III — contains physodic and 2′-O-methylphysodic acids. The chemotype III was shown to be associated with a specific substrate. The composition of secondary metabolites was determined for the first time for H. subduplicata. The species is represented by two chemotypes: I — contains vittatolic acid, 3-hydroxyphysodic and physodic acids; II — contains 3-hydroxyphysodic, physodic acids and lividic acid. The latter was not previously reported for the genus Hypogymnia.