Salvia stenophylla Burch. ex Benth. (Lamiaceae) is a perennial aromatic herb, which is widespread in the high altitude areas of the central and eastern parts of South Africa. It is closely related to Salvia runcinata L. f. and Salvia repens Burch. ex Benth. with which it forms a species complex. Taxonomically, distinction between the three taxa is problematic. Salvia stenophylla is economically important as a source of alpha-bisabolol used in aromatherapy and active cosmetic formulations. The fresh aerial parts of the three taxa obtained from 25 natural populations were hydrodistilled to isolate the essential oil and analytical assessment of the oil was carried out using gas chromatography coupled to mass spectroscopy (GC/MS). The GC/MS results showed variation in the qualitative and quantitative chemical composition within and between populations of the same and different taxa. The dominant compounds in the S. stenophylla oils include: alpha-bisabolol (46.5%), limonene (38.1%), delta-3-carene (24.9%), gamma-terpinene (20.3%), p-cymene (18.4%) and (E)-nerolidol (53.6%). Salvia repens oils accumulated major compounds like (E)-nerolidol (25.2%), ledol (25.4%), camphor (12.7%), beta-caryophyllene (13.6%) and beta-phellandrene (22.2%). Salvia runcinata oils had (E)-nerolidol (72%), alpha-bisabolol (41.1%), limonene (24.1%), alpha-pinene (45%) and beta-pinene (15%) and 26% of guaiol in high percentages. Seven chemotypes were identified and they were used to investigate the chemotaxomic relationships in the species complex. The results suggested that S. stenophylla and S. repens are the closest allies within the complex.