BackgroundArtemisia saharae Pomel is a new taxon of Artemisia herba-alba Asso (Asteraceae) which is endemic to Tunisia and Algeria. This shrub, commonly known as white wormwood or desert wormwood, is largely used in folk medicine and as a culinary herb. The bulks aromatic plants come from wild populations whose essential oils compositions as well as their biological properties are severely affected by several factors such as geographic conditions. Therefore, the aim of the present work is to provide more information about the influence of altitude variation on the essential oil composition, antimicrobial and antioxidant properties of Artemisia saharae growing wild in the same geographical area.ResultsEssential oils were extracted by hydrodistillation of leaves and flowers of the plant collected from seven different altitudes of the Baten Zamour region (southwest of Tunisia). The highest essential oil yields (2.70-2.80%) were obtained for populations of high altitudes.Seventy-five compounds, representing 92.78 to 96.95% of the total essential oils, were separated and identified. Essential oils were characterized by very high percentage of oxygenated monoterpenes (52.1–72.6%) which constituted the predominant class. From the analyzed populations, the major compounds (>7%) were α-thujone, β-thujone, chrysanthenone, camphor, chrysanthenyl acetate, and sabinyl acetate. Sabinyl acetate which was detected in some populations at relatively high percentages (7.7–10.8%) seems to be characteristic to Southern Tunisian A. saharae. The studied essential oil showed a chemical diversity depending on the population altitude as revealed by linear discriminant and cluster analyses.ConclusionsThree population groups associated with altitudinal levels were distinguished. It is worthy to note that the most discriminating compounds of chemical groups were the minor ones. Despite the high variation of essential oil compositions, the high altitude population did not affect severely the antibacterial activity against the most tested strains. Altitude seems to be an important factor influencing the yield and the chemical profile of Artemisia saharae essential oils. Knowledge of the chemical composition of essential oils in relation to environmental factors is a very important quality criterion for their marketing and contributes to their valorization as functional ingredient in food technology.Electronic supplementary materialThe online version of this article (doi:10.1186/s40529-014-0076-0) contains supplementary material, which is available to authorized users.