Abstract: The majority of PCR-based fingerprinting technologies generate dominant genetic markers; homozygote present and heterozygote genotypes cannot be distinguished using conventional detection methods. In contrast, codominant genetic markers provide an unambiguous distinction among each genotype. A genotyping method is described that includes procedures implemented in software. This method quantifies allele copy number and enables recovery of codominant genotypes from markers expressing ostensibly dominant phenotypes. These procedures are designed and implemented to (1) greatly reduce variability attributable to sample assay and detector noise, (2) accurately estimate allele size and copy number, (3) provide normalization criteria for intra- and inter-marker comparisons, and (4) scale the resulting data to determine the genotype of individual markers.