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Microsatellites are abundantly present in nuclear genome. They are renowned for their utility in polymorphism analyses. The informativeness of multilocus ISSR (Inter-simple sequence repeats) markers was compared to analyze the Arabian horse breeds (Equus caballus) including Middle Eastern Arabian (28) and mixed (hybrid) Arabians (10). They are helpful in the assessment of genetic diversity among horse populations. The marker (GA)9C gave 18 alleles in electrophoretic agarose gel. The low numberfatcat:cphvlfgxwfckrp2qcpwx3n4qgy