[show abstract][hide abstract] ABSTRACT: Aplochiton zebra (peladila, zebra trout) is a galaxiid fish endemic to Patagonia and the Falklands Islands, where populations are threatened by salmonid introductions. Here we describe the isolation and characterization of 13 polymorphic microsatellite DNA markers that can be used for assessing the genetic variation and conservation status of this species. The variability of these markers was assessed in six rivers in Chilean Patagonia. The number of alleles ranged from 5 to 80 per locus and observed heterozygosities varied between 0.168 and 0.910. A protocol for multiplexing these markers is described.