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Amplified fragment length polymorphism (AFLP) was used to analyze the genetic diversity of domestic stocks of channel catfish (Ictalurus punctatus). Sixteen populations within Alabama (USA) were surveyed using five primer combinations. A total of 454 reproducible, polymorphic bands were detected from 282 individuals, with an average heterozygosity of 0.135. The percentage of polymorphic loci varied greatly within distinct populations, ranging from 18.26% to 100%. Research populations tended to have a lower percentage of loci polymorphic than farm populations. The estimated average Fst value across all loci was 0.4456. However, this value dropped to 0.1763 when the Hicks Farm stock was excluded from the analysis. Cluster analysis by Jaccard''s pairwise similarity coefficient indicated high similarity among individuals, with some population-specific clusters and with the Hicks Farm stock being highly distinctive. Nei''s population-wise identity measures found all populations except the population from the Hick''s Farm related with 96% similarity. The Hick''s Farm stock was 34% similar to the other populations. The genotypic information derived from this study is consistent with the historical origins and management of catfish broodstocks. The results of this study suggest that many channel catfish farm strains in Alabama are genetically similar, but some very distinct differences exist. Such information has implications for future broodstock selection and management and for further analysis of interactions between domestic and wild populations of channel catfish. [Copyright &y& Elsevier]