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DNA marker technologies have revolutionized the way aquaculture genetics research is being conducted (Liu and Cordes 2004). Early on, most applications of molecular genetics in aquaculture relied on the estimation of demographic parameters of diversity and differentiation that were derived from averaging the genetic composition over populations or stocks. It has been recognized for nearly 25 years, however, that further knowledge of relevance for stock management and production may be obtained from the analysis of individual-based genotypic information (Smouse et al. 1982). The blooming development of new genetic markers over the last decade, namely variable number of tandem repeat loci (especially microsatellites), Amplified Fragment Length Polymorphism (AFLP), and Single Nucleotide Polymorphism (SNP) have revived a major interest in studies based on the definition of individual multilocus genotypes, and opened exciting avenues of research and applications. Basically, studies of relevance for aquaculture and based on the analysis of individual multilocus genotypes can be grouped into three broad categories of applications: parentage (including kinship), group allocation, and hybrid detection. Parental allocation studies necessitate the assessment of parental relationships within populations, which may be achieved in various ways, including the use of exclusion probability, likelihood methods, and categorical and fractional parental assignment (reviewed in Wilson and Ferguson 2002, Jones and Ardren 2003). Parental allocation improves the efficiency of selective breeding programs in many ways, namely the following: