Premise of the study:Microsatellite markers can be used to evaluate population structure and genetic diversity in native populations of Indigofera pseudotinctoria (Fabaceae) and assess genetic disturbance caused by nonnative plants of the same species.Methods and Results:We developed 14 markers for I. pseudotinctoria using next-generation sequencing and applied them to test two native populations, totaling 77 individuals, and a transplanted population, imported from a foreign country, of 17 individuals. The mean number of alleles was 3.310, observed heterozygosity was 0.242, and expected heterozygosity was 0.346. The fixation index in the transplanted population was 0.469, which was higher than in the native populations (0.154 and 0.158). In addition, the transplanted population contains one allele that is not shared by the native population.Conclusions:Microsatellite markers can be useful for evaluating genetic diversity within and between populations and for studying population genetics in I. pseudotinctoria and related species.