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This study analyzed the effect of organic solvent extractives on the classification of wood species via near-infrared spectroscopy (NIR). In our previous research, five species of Korean softwood were classified into three groups (i.e., Cryptomeria japonica (cedar)/Chamaecyparis obtuse (cypress), Pinus densiflora (red pine)/Pinus koraiensis (Korean pine), and Larix kaempferi (Larch)) using an NIR-based principal component analysis method. Similar tendencies of extractive distribution were observed among the three groups in that study. Therefore, in this study, we qualitatively analyzed extractives extracted by an organic solvent and analyzed the NIR spectra in terms of the extractives’ chemical structure and band assignment to determine their effect in more detail. Cedar/cypress showed a similar NIR spectra patterns by removing the extractives at 1695, 1724, and 2291 nm. D-pinitol, which was detected in cedar, contributed to that wavelength. Red pine/Korean pine showed spectra changes at 1616, 1695, 1681, 1705, 1724, 1731, 1765, 1780, and 2300 nm. Diterpenoids and fatty acid, which have a carboxylic group and an aliphatic double bond, contributed to that wavelength. Larch showed a catechin peak in gas chromatography and mass spectroscopy analysis, but it exhibited very small NIR spectra changes. The aromatic bond in larch seemed to have low sensitivity because of the 1st overtone of the O-H bond of the sawdust cellulose. The three groups sorted via NIR spectroscopy in the previous research showed quite different compositions of extractives, in accordance with the NIR band assignment. Thus, organic solvent extractives are expected to affect the classification of wood species using NIR spectroscopy.