Following the first suggestion of inherent molecular chirality in asymmetrically substituted subphthalocyanines by Torres and co-workers in 2000, elucidation of the relationship between structure and chirality has become an important issue. However, separation of the enantiomers has been prevented by the low solubility of the molecules synthesized to date, and it has not been possible to link the CD signs and intensities to their absolute structures. Recently, we observed that 1,2-subnaphthalocyanines possess two diastereomers with respect to the arrangement of the naphthalene moieties and that these novel chiral molecules exhibit moderate solubility in common organic solvents. This has enabled us to separate all of the diastereomers and enantiomers. The two diastereomers have been completely characterized by NMR spectroscopy and X-ray diffraction analysis. The absorption and magnetic circular dichroism spectra, together with theoretical calculation, reveal a small variation in the frontier molecular orbitals of the 1,2-subnaphthalocyanines compared with conventional subphthalocyanines, except for destabilization of the HOMO–3, which results in a characteristic absorption in the Soret band region. The chirality of 1,2-subnaphthalcyanines, including the CD signs and intensities, is discussed in detail for the first time with enantiomerically pure molecules whose absolute structures have been elucidated by single-crystal X-ray diffraction analysis.