FT-IR spectroscopy, combined with multivariate analysis, was used to determine whether 67 different wild and rootstock peach accessions could be discriminated from each other. Genomic DNA was isolated from leaves, and the purified genomic DNA was analyzed by FT-IR spectroscopy in the spectral region from 1800 to 800 cm^-1. FT-IR spectra showed that typical spectral differences existed in the frequency regions of N-H stretching (amide I), C=O stretching vibrations (amide II), and PO₂⁻ ionized asymmetric and symmetric stretching. Principal component analysis (PCA) was able to discriminate three groups. The partial least squares discriminant analysis (PLS-DA) yielded more clear discrimination among the three groups of peach accessions. The FT-IR spectral differences might be directly related to subtle changes in the base functional group and backbone structures of genomic DNA. This technique could provide a research foundation for FT-IR spectral-based rapid diagnosis, selection, and discrimination of peach accessions for rootstock.