The Texas tortoise (Gopherus berlandieri) is a state-protected, threatened species in Texas. The expansion of agricultural practices and urban development are major causes of habitat degradation for the species. To provide genetic data that can inform conservation planning for this species, genetic variation, population structure, and the process that maintains the observed structure were examined in the Texas populations of G. berlandieri. Microsatellite genetic variation of 8 polymorphic loci was examined for a total of 138 individuals collected from 10 sampling areas in southern Texas. Assignment tests, F statistics, and analysis of molecular variance indicated that G. berlandieri forms weak population differentiation into northern and southern groups, with a boundary at southern Duval County. A test of isolation by distance and indirect estimation of the number of migrants (Nm) suggest recent gene flow between the 2 groups. Estimation of the extent of contemporary migration appears to be complicated by human translocation of tortoises, and an asymmetrical direction of migration needs further examination. Gopherus berlandieri is weakly differentiated because of ongoing migration as evidenced by a pattern of isolation by distance. Given the limited population structure and continuous habitat degradation, designation of 2 management units may not be warranted. Conservation efforts, rather, should emphasize connectivity between the groups to maintain genetic variation in both groups.