The genus Mangifera has long been used in traditional medicine, particularly the bark. However, ethnopharmacological studies on Mangifera bark are generally limited to single-species investigations and have not integrated quantitative chemical analysis with conservation implications. This research aims to comparatively analyze the chemical compound profiles of the bark of three endemic Mangifera species from Kalimantan, namely Kasturi (Mangifera casturi), Cuban, and Palipisan, and relate them to ethnopharmacological values and utilization-based conservation. Bark extracts were analyzed using gas chromatography–mass spectrometry (GC–MS). The identified compounds were grouped based on their chemical structure and biological function. Venn diagram analysis was used to evaluate the similarities and uniqueness of compounds across species, which were then interpreted in the context of ethnopharmacology. A total of 27 compounds were identified, dominated by saturated and unsaturated fatty acids, fatty acid esters, and complex lipids. Palmitic acid was the dominant compound in all species, followed by oleic acid and other fatty acid derivatives. The Venn diagram analysis showed that most of the major compounds were located across the three species, indicating functional chemical redundancy, while minor compounds formed species-specific chemical fingerprints. The similarities in key chemical profiles explain the ethnopharmacological basis for interspecies substitutive use in traditional medicine, while variations in relative composition and the presence of species-specific compounds have the potential to influence the spectrum of biological activity. These findings are expected to provide a basis for further research on bioactivity and safety testing while strengthening conservation approaches based on the use of non-timber forest products to support the preservation of endangered endemic species.