Hexagonal chains are a special class of catacondensed benzenoid system and phenylene chains are a class of polycyclic aromatic compounds. Recently, A family of Sombor indices was introduced by Gutman in the chemical graph theory. It had been examined that these indices may be successfully applied on modeling thermodynamic properties of compounds. In this paper, we study the expected values of the Sombor indices in random hexagonal chains, phenylene chains, and consider the Sombor indices of some chemical graphs such as graphene, coronoid systems and carbon nanocones.