Social mating systems (e.g., monogamy, polygamy, or polyandry) are relatively stable behavioral strategies developed by environmental in animals, but the genetic imprint of a particular mating system is often incongruent with the social mating system due to extrapair matings. However, the genetics of mating systems remain little understood in rodents. In this study, we investigated the genetic signature of the mating system of 141 (63 females, 78 males) field-captured Midday Gerbils (Meriones meridianus) -a rodent species commonly found in the Minqin Desert in China-through microsatellite site analyses of genetic structure and relatedness. Seven pairs of highly polymorphic microsatellite loci were selected and were highly polymorphic, the combined exclusion probability was greater than 0.99. The parent pair paternity test by Cervus 3.0 software show that, eleven mother-offspring and nine father-offspring relationships were identified in 2018, involving 26 individuals from 10 families. Similarly, 19 mother-offspring and 19 father-offspring relationships were identified in 2019, involving 48 individuals from 18 families. All three types of genetic mating structure were identified: monogamy (19 families), polyandry (4 families), and polygyny (5 families), providing evidence that the genetics underlying mating systems in this species are variable, can be incongruent with behavioral evidence for social mating systems, and could vary based on environmental cues, including degree of perceived or actual predation.