Genetic markers using multilocus probes or primers benefit from the fact that multiple polymorphisms, representing various genomic regions, are generated simultaneously. However, a major drawback is that in general the band profiles cannot be interpreted in terms of loci and alleles, but are scored as the presence or absence of bands of a particular size. As a consequence, similar sized fragments may represent alleles from different loci and not be homologous. Therefore, locus-specific markers should be considered for questions of phylogeny or genetic relatedness. Alternatively, markers for fingerprinting studies rely on differences only, and homology is not a concern. In general, locus-specific markers generate polymorphisms of known identity, however in most cases sequencing data are needed for their development.