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We review the literature to provide examples of how molecular pedigree analysis has been used extensively to examine patterns of distribution, dispersal, and social behaviour in fishes and how it provides a tool for the estimation of quantitative genetic parameters. Although multiple methodologies can be used to examine family structure, the efficacy of any molecular pedigree analysis is generally dependent on prior consideration of interrelated statistical and biological factors. Statistical issues stem from the choice of molecular marker type and marker set used, in addition to sampling strategy. We discuss these considerations and additionally emphasize the utility of supplemental nongenetic data for increasing the efficacy of pedigree analysis. 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