Microsatellites are useful markers to address questions of recent gene flow, given that they are relatively neutral to natural selection and show high levels of variability. To date, only one study has used these markers to answer ecological questions in the speciesrich lizard genus Liolaemus. Here, we use microsatellite loci to estimate population structure, paternity, and effective size of a population of L. xanthoviridis. The study took place in Isla Escondida Bay, Chubut (Argentina), during four spring-summer seasons (2012–2015). We marked and sexed 227 captured individuals and transported 10 gravid females to our laboratory. Digits of marked lizards were used for molecular work, and we resolved eight microsatellite loci to characterize genetic diversity, paternity, and population structure. We found no evidence of multiple paternity, and our samples constitute a single genetic population of L. xanthoviridis. Our results show that genetic diversity is higher in L. xanthoviridis than in many other species of lizards we found in the literature. Such high genetic diversity is important given the restricted geographic distribution of this species.