In order to facilitate high throughput genotyping of zebrafish, we have developed a novel technique that uses High Resolution Melting Analysis (HRMA) to distinguish wild-type, heterozygous mutants and homogyzous mutants. This one hour technique removes the need for restriction enzymes and agarose gels. The generated melting curve profiles are sensitive enough to detect non-specific PCR products. We have been able to reliably genotype three classes of mutations in zebrafish, including point mutants, apchu745 (apcmcr), and p53zy7 (p53I166T), a small deletion mutant (bap28 y75) and a retroviral insertion mutant (wdr43hi821a). This technique can genotype individual zebrafish embryos and adults (by tail-clip) and is applicable to other model organisms. © 2009 Wiley-Liss, Inc.