Spotted seatroutCynoscion nebulosus(N= 674) from 12 geographic populations along the Texas and northern Mexico Gulf coasts were surveyed to determine population structure as indicated by the distribution of electrophoretically detectable allelic variants. The percentage of polymorphic loci among 44 putative gene loci averaged 15.5% and ranged from 13.6 to 15.9%. The percentage of heterozygous loci per individual (H) for all loci averaged 1.6% and ranged from 1.2% in East Matagorda Bay to 2.3% in Rio Soto La Marina. A cline existed in the frequency of thesAAT-2*80allele (for aspartate aminotransferase) (0.9–17.1%) and in average individual heterozygosity with respect to degrees north latitude and west longitude, Heterogeneity tests indicated allele counts at thesAAT-2 *locus were distributed heterogeneously among the 12 localities. Subpopulation differentiation was low (FST= 0.012), and quantitative (Nem) and qualitative estimators suggested high gene flow throughout this study area. The correlogram of mean spatial autocorrelation coefficients of allele frequencies indicated response surfaces with short-distance, positive autocorrelation coupled with long-distance negative correlation. This finding conforms well to the spatial patterns expected under an “isolation-by-distance” population model. This study did not provide evidence of independent subpopulations (stocks) of spotted seatrout within Galveston Bay, as previously had been suggested, or among Texas bays, as had been suggested for Florida bays. A westerly directed, nearshore egg and larval transport system moving along the series of closely spaced bay systems may facilitate spotted seatrout gene exchange between Texas bay populations. Enzyme systems coded by rare alleles were identified and could prove useful as genetic markers in a spotted seatrout stocking program.