Low levels of genetic variability, inbreeding, and limited gene flow are three possible threats to small, isolated plant populations as exemplified by Quercus hinckleyi C.H. Muller. J. This scrub oak species has survived over the past 10,000 years in a region in which the climate has become increasingly xeric. While more prevalent after the last ice age, its US range is now limited to a handful of populations in one county in West Texas. This study examines the genetic diversity of the relict metapopulation and resultant conservation implications. We used microsatellites to genotype a total of 204 ramets collected from three locations in Presidio County, TX, that represent all known occurrences of Q. hinckleyi. Analyses of eight loci were used to determine levels of genetic variability, population structure and clonal growth. Genetic diversity for the sampled plants was high: for the total metapopulation, the mean number of alleles (Na) was 17.875; the mean observed heterozygosity (Ho) was 0.807; and the mean expected heterozygosity (He) was 0.853. Allelic richness by locus and sample (Rs) ranged from 5.15 to 14.73. We found no evidence of inbreeding as measured by the fixation index, FIS. Population structure analyses showed two distinct subpopulations with significant differentiation, as shown by GST (0.033, Bonferroni corrected P = 0.001) and DJOST (0.451, Bonferroni corrected P = 0.001), unique alleles and genetic clustering. High clonality was discovered at the two smallest sites, with only seven unique genotypes among 58 ramets sampled. One clone was over 30 m across. Sexual reproduction appears to be present at the other sites, as indicated by less extensive cloning. Overall, we found that Q. hinckleyi is not genetically depauperate despite its rarity, although unique genets are reduced because of cloning. Asexual reproduction may in fact have allowed the small relict populations to survive extreme environmental change as their range has dwindled. The level of genetic diversity and differentiation among the remaining Q. hinckleyi sites warrants protection and preservation of all.