The zebrafish species Danio rerio has become one of the major vertebrate model organisms used in biomedical research. However, there are aspects of the model that need to be improved. One of these is the ability to identify individual fish and fish lines by DNA profiling. Although many dinucleotide short tandem repeat (diSTR) markers are available for this and similar purposes, they have certain disadvantages such as an excessive polymerase slippage ("stutter") that causes difficulties in automated genotyping and cross-laboratory comparisons. Here we report on the development of a 13-plex of tetranucleotide and pentanucleotide STRs (tetraSTRs and pentaSTRs, respectively) that have low stutter. The system uses an inexpensive universal primer labelling system, which can easily be converted to a direct labeling system if desired. This 13-plex was examined in three zebrafish lines (NHGRI-1, kca33Tg, and kca66Tg, originally obtained from ZIRC). The average observed heterozygosity (Ho) and expected heterozygosity (He) in these highly inbred lines were 0.291 and 0.359, respectively, which is very similar to what has been found with diSTRs. The probability of identity (PI) for all fish tested was 2.1 × 10 −5 and the PI for siblings (PIsib) was 6.4 × 10 −3 , as calculated by the Genalex package. Ninety percent of the fish tested were correctly identified with their respective strains. It is also demonstrated that this panel can be used to confirm doubled-haploid cell lines. This multiplex should find multiple uses for improving the accuracy and reproducibility of studies using the zebrafish model. Zebrafish (Danio rerio) is the vertebrate animal model most rapidly adopted in biomedical research. The zebrafish genome is 70% similar to the human, and 80% percent of the genes responsible for human diseases have an orthologue in zebrafish 1. It is relatively easy to generate mutant animals, and the cost of zebrafish maintenance is low. Applications of this animal model include, among the many, toxicology, developmental biology, genetics and degenerative diseases, psychiatric conditions, cancer, and metabolic disorders. Researchers can choose from a variety of wild-type and mutant zebrafish lines for their studies. All available from the Zebrafish International Resource Center (ZIRC), wild-type zebrafish lines include Tübingen, AB, NHGRI-1, Sanger AB Tübingen (SAT), WIK, Tüpfel long fin (TL), Nadia, and Cooch Behar. Also available, are more than forty thousand mutant lines. Despite previous reports of the derivation of the IM inbred zebrafish line in 2011, homozygous zebrafish lines for all loci are lacking 2,3. Some initiatives are in progress that may fulfill the need for fish lines that have an identical genetic identity. We are currently working on a strategy to generate homozygous diploid fish using the method developed by Streisinger and colleagues in 1981, followed by somatic cell nuclear transfer (SCNT) 4-9. Once a gynogenetic embryo is developed, we isolate cells from them, and subsequently, after testing for normal k...