To investigate the population structure of the obligate plant-ant Pseudomyrmex ferrugineus, we developed primers for 12 microsatellite loci. We tested the variability of the markers on 11 individuals from each of two populations (totalling 22 individuals) and found two to 12 alleles per locus and population. No deviations from Hardy–Weinberg equilibrium were detected. Observed and expected heterozygosities at each locus ranged from 0.00 to 0.50 and from 0.08 to 0.46, respectively. We also investigated suitability of these primers in two congeneric species.