The Alpine marmot Marmota marmota is a territorial rodent. Resident adults regularly scent-mark their territory by cheek-rubbing, mainly on burrow entrances and along boundaries. The purpose of this three part study was to gain further insight into this scent-marking behavior by: (1) observing the response of free-ranging marmots to foreign scent marks, (2) confirming the glandular source of the marking substance by histologic examination of the temporal gland, and (3) identifying biologically active chemical fractions of the marking substance. To allow field tests, we developed a device consisting of a glass tube placed upside down over a stake. Two devices were simultaneously placed at one burrow entrance. On one device, a clean tube was used and, on the other, a tube alternatively coated with either whole natural scent-marking substances or various fractions obtained by solvent extraction or chromatographic separation from whole scent-marking substances. Subsequent observations showed a significant difference in the duration of nose contact and number of cheek-rubbing movements. Resident adult marmots sniffed and marked tubes bearing alien marks significantly more than clean control tubes. Similar differences in behavior were observed with ethanol extracts of whole scent-marking substances. Extracts obtained with pentane and dichloromethane showed no bioactivity, suggesting that highly polar compounds are the active substances in the Alpine marmot. The temporal gland is an exocrine gland located on each side of the head with numerous pores opening at the surface of the skin in the cheek area GC-MS analysis of individually collected samples from these glands showed that over 30 compounds were consistently present. Seven of these compounds were identified. Two fractions were obtained and used together and separately in field tests. Fraction 1 was composed mainly of short-chain alcohols and alkanes, and fraction 2 had a more acid and ester composition. The fact that these two fractions were active together but not separately strongly suggests that the active territorial signal results from a synergistic interaction between several compounds.