Genetic diversity, population structure, average long-term effective population size (Ne), and average long-term genetic migration rate of red drum Sciaenops ocellatusin each of four Texas bays were assessed using variation in 13 nuclear-encoded microsatellites among samples from the 2004 and 2005 cohorts. No significant differences in genetic diversity were detected among bays. Levels of gene diversity of red drum in each bay were equal to or greater than estimates reported for microsatellites in red drum sampled previously from two of the four bays and from other bays in the southeastern USA, including some that had not yet been supplemented with hatchery-raised fish. Tests of the homogeneity of allele and genotype distributions (including analysis of molecular variance) among the four bays were nonsignificant. Estimates of the migration rate (m) between bays ranged from 0.08% to 0.15%, with the average long-term number of migrants (calculated as Ne× m) between bays estimated to range from 1.04 to 2.37 fish/generation. Estimates of average long-term Nein the four bays ranged from 1,302 to 1,581 fish and collectively were well within the range hypothesized to support sustained, long-term persistence. The estimates of Nealso were, on average, five to six times higher than comparable estimates reported for the 1986–1989 red drum cohorts sampled from seven bays across the northern Gulf of Mexico. Adjustment of long-term Nein each of the four bays relative to bay-specific spatial parameters revealed a positive relationship with red drum abundance as measured by catch-per-unit-effort statistics compiled by the Texas Parks and Wildlife Department between 1982 and 2005. The observed high levels of genetic diversity, estimates of average long-term Ne, and increased Neover the past 15–20 years are consistent with the hypothesis that the Texas Parks and Wildlife Department's stock enhancement program has not genetically compromised the resident red drum subpopulations in the four bays.