We have developed and now use DNA-based identification of catfish in order to produce pedigreed research populations. Identification of catfish individuals and families allows us to co-culture catfish at a young age, and this reduces environmental effects that confound estimates of genetic potential. We have also produced genetic maps and genome sequence assemblies to facilitate the identification of genomic regions that control important production traits. Genetic markers derived from these resources will be useful for screening potential broodstock to identify those that contain “positive” genetic sequences that will lead to improved performance. Genomic-based analyses are also being used to better understand the beneficial and pathogenic microorganisms that affect catfish production.