A new method is presented for measuring microfibril angles (MFAs) from transverse tree sections by using polarized optical microscopy combined with a liquid-crystal tunable filter. The MFA transition analysis of tree growth rings via generalized two-dimensional correlation is proposed. The unique features of two anatomically similar Cupressaceae species, Chamaecyparis obtusa S. & Z. and Thujopsis dolabrata S. & Z. and its variant, were extracted through MFA analysis. The technique efficiently visualized MFA distributions under wide field observation and uncovered seasonal differences. Classification results of supervised models exhibited 60% accuracy, despite featureless cross-sections of the conifers. Overall, MFA is a promising index that can identify specific features of wood species.