Baccharis dracunculifolia DC. and Baccharis microdonta DC. (Asteraceae) are woody species morphologically similar growing in Uruguay, where not taxonomists people often confuse them in field conditions. As the essential oil of B. dracunculifolia (‘vassoura’ oil) is highly prized by the flavor and fragrance industry, the correct differentiation of the two species is a key factor in exploiting them profitably and reasonably. To differentiate both Baccharis species, in this work their volatile expression profiles were studied as an alternative tool to determine authenticity and quality. Volatile organic compounds (VOCs) were monthly extracted during an entire year from aerial parts of wild populations by simultaneous distillation extraction (SDE), and studied by gas chromatography/mass spectrometry (GC/MS; identification) and conventional gas chromatography (GC‐FID; component abundances determination). Enantioselective gas chromatography/mass spectrometry (Es‐GC/MS) was applied in the search of parameters able to ensure genuineness of each species extract. Qualitative VOCs profiles were found to be similar for both species, being β‐pinene, limonene, spathulenol, caryophyllene oxide, and viridiflorol the main components. However, the abundance of those VOCs were two to ten times higher in B. dracunculifolia than in B. microdonta during the year of study. These Baccharis spp. showed species‐specific patterns of VOCs expression according to the seasonality, and interestingly, oxygenated compounds (trans‐pinocarveol and myrtenal) increased their abundances at full‐flowering stages. The enantiomeric distribution of selected monoterpenes (α‐ and β‐pinenes, limonene, linalool, terpinen‐4‐ol, and α‐terpineol) presented differential values for both Baccharis spp., meaning that Es‐GC might be a useful tool for differentiating chemically both species in Uruguay for genuineness determination purposes.