Scent-marking is widespread among mammals and conveys various information to conspecifics, such as territoriality, social hierarchy and reproductive status. To investigate whether marking behavior is influenced by spatial proximity and kinship in Mongolian gerbils (Meriones unguiculatus), we collected data from a wild free-living population of Mongolian gerbils in Zhenglanqi, Xilingol League, Inner-Mongolia, China. Using the capture-mark-recapture method, we conducted urine-marking behavior tests between gerbils living in different social groups from April to October in 2014. The distance between burrow systems was calculated using the Pythagorean theorem, and pairwise genetic relatedness was estimated using microsatellite DNA markers by ML-RELATE software. Generalized linear mixed effects analysis revealed that neither spatial nor genetic distance had significant effects on the intensity of urine marking in males, and it was same for females during breeding season. However, during the food-hoarding season, the genetic distance significantly affected the intensity of urine marking in females, and there was a significant interaction between spatial and genetic distance. Our results imply that urine-marking behavior of Mongolian gerbils is influenced by kinship and spatial proximity, which may match the breeding or food-hoarding traits in Mongolian gerbils.