Aliphatic hydrocarbons were analyzed in 3 species (Cladonia vulcani, Cladonia scabriuscula, and Xanthoria sp.) of lichens collected from Hokkaido and Hyogo Prefectures, Japan. Molecular composition of n-alkanes is likely influenced by precipitation, as the long chain n-alkanes are produced under arid environments. Alkenes such as heptadecene are also detected as major components in these samples. Molecular composition of these alkanes is different between the genus Xanthoria and Cladonia, suggesting that the composition is influenced by taxonomic diversity. Molecular composition of the aliphatic hydrocarbons other than n-alkanes and alkenes detected are far different between the genera Xanthoria and Cladonia, but are almost similar in these 2 species of the genus Cladonia, potentially depending on taxonomy at the genus level. From these results, we predict that the alkenes, as well as other aliphatic hydrocarbons, can be useful as a chemotaxonomic marker, while the composition of n-alkanes can be an environmental indicator.