Scent-marking is a frequent behaviour of highly social ground squirrels and might play an important role in their social dynamics. Female Columbian ground squirrels exhibit considerable scent-marking during the reproductive period. We examined how gestating and lactating females responded to jugal gland scent-marks of same-sexed and opposite-sexed conspecifics with attention to genetic relatedness and the geographical location of the territory of individuals. We tested the dear-enemy, threat-level and kin-discrimination hypotheses to explain patterns of scent-marking. Females sniffed the scent of non-neighbouring males significantly longer than other types of scent categories and tended to over mark the scent of females more than the scent of males. Furthermore, females sniffed significantly longer at scents during gestation than during lactation. We concluded that scent-marking mainly functioned in the defence of female territories and for protection of pups against infanticidal females (threat-level hypothesis). Our results were also in accordance with the kin-discrimination hypothesis, because greater attention was paid to the marks of non-kin females. Kin females might not pose an infanticidal threat, perhaps explaining greater tolerance among related reproductive females. We concluded that scent-marking may be a relatively low-cost means of territorial defence, as well as a means of communication of aspects of individual identity.