Brassicaceae is a family of vegetables found all over the world that has been attracting the attention of researchers due to its rich chemical composition and potential health benefits (antioxidant and anti-inflammatory, as well as antimutagenic activity and potential anticarcinogenic effects). In Italy, various Brassicaceae varieties are commercially available, including traditional local cultivars, which have unique features and genetic diversity. As a result, there is a growing need to protect and recognize these landraces to preserve biodiversity. In this study, non-destructive tools such as Attenuated Total Reflectance-Fourier Transform-Infrared Spectroscopy (ATR-FT-IR) and chemometrics were employed to investigate eight distinct Brassicaceae landraces. The collected data were analyzed using a class modeling approach (Soft Independent Modeling of Class Analogy) and a discriminant classification method (Partial Least Squares Discriminant Analysis) to assess similarities and dissimilarities among the samples, all cultivated in an experimental field under the same pedoclimatic conditions. Remarkably, the combination of IR spectra and chemometric tools allowed accurate classification of the samples according only to their genetic background and despite their inclination to hybridization. The study highlights and demonstrates the importance and applicability of this specific non-destructive method for assisting the management and preservation of the genetic resources related to the local varieties of Brassicaceae.