Hybridization of the box turtles Terrapene carolina and T. ornata has been reported throughout their sympatric range. Herein, eight polymorphic microsatellite loci and one mitochondrial polymorphism were used to assess patterns of introgression between these two species, both of which are of conservation concern. We estimated standard population statistics, population assignments, and ancestry for 28 T. carolina, 17 T. ornata, and ten putative T. carolina–T. ornata hybrids from southwest Texas. Both parental populations had high observed heterozygosity and allelic diversity, and there was high gene flow between the two parental species. Ancestry values were sporadic and typical of species that have been hybridizing. Approximately 86% and 76% of T. carolina and T. ornata, respectively, were correctly assigned to their species. Seven of the hybrids had a high level of ancestry for T. carolina and three resembled T. ornata. Interestingly, all T. carolina, putative hybrids, and one T. ornata had haplotypes of T. carolina, whereas all but one T. ornata had haplotypes of T. ornata. These results suggest that hybridization has occurred for several generations within this population, and we discuss how such hybridization may influence population structure for such species of concern.