The reproducibility, mode of inheritance and polymorphism of amplified fragment length polymorphism (AFLP) markers were examined in ayu Plecoglossus altivelis (Salmoniformes: Plecoglossidae). The AFLP markers were highly reproducible, their inheritance following Mendelian expectations. The number of fragments amplified (34-134), polymorphic ratio (0Á15-0Á78) and average heterozygosity (0Á02-0Á25) of the AFLP markers showed significant variation among six primer pairs and among ayu populations, including a landlocked LakeBiwa population, two amphidromous populations (P. a. altivelis) and two Ryukyu-ayu populations (P. a. ryukyuensis). Although AFLP analysis provided similar results in intra-population diversity and relationships among populations to those found by analyses of allozymes, microsatellites and mitochondrial DNA sequences, AFLPs showed higher polymorphisms and hence greater distinction between genetically close populations. # 2005 The Fisheries Society of the British Isles