Aquaculture International 12: 19–32, 2004. © 2004 Kluwer Academic Publishers. Printed in the Netherlands. Genetic introgression between Arctic charr (Salvelinus alpinus) and brook trout (Salvelinus fontinalis) in Bavarian hatchery stocks inferred from nuclear and mitochondrial DNA markers RIHO GROSS 1,∗ , BERNHARD GUM 2 , REINHARD REITER 3 and RALPH KÜHN 2 1 Institute of Animal Science, Estonian Agricultural University, 1 Kreutzwaldi St., EE-51014 Tartu, Estonia; 2 Wildlife Biology and Management Unit, Department for Ecosystem and Landscape Management, Technical University Munich-Weihenstephan, D-85354 Freising, Germany; 3 Bayerische Landesanstalt für Fischerei, D-82319 Starnberg, Germany; ∗ Author for correspondence (e-mail: rgross@eau.ee; phone: +372-7-313489; fax: +372-7-313429) Received 15 November 2002; accepted 20 June 2003 Abstract. Nuclear insulin-like growth factor 2 gene (IGF-2), growth hormone 1 gene (GH-1) and internal transcribed spacer 1 (ITS-1) of the ribosomal DNA as well as the mitochondrial NADH-3 and NADH-4 dehydrogenase genes (ND-3/4) exhibited species-specific restriction fragment patterns and three microsatellite loci (Sfo18, Ssa85 and Ssa197) had non-overlapping allele size ranges in Arctic charr and brook trout and were used as diagnostic markers for testing genetic purity of hatchery stocks and wild populations of Arctic charr and brook trout in Bavaria, Germany. Screening of four wild populations (three in Arctic charr and one in brook trout) revealed only a single hybrid (back-cross to brook trout) individual in L. Starnberg. In contrast, in three (out of five) hatchery stocks of Arctic charr and in both hatchery stocks of brook trout hybrids were detected with the frequency from 3 to 100%. Three hatchery stocks (SS2, SA and BS1) represent a hybrid swarm because they contained a very high proportion of hybrids (from 83 to 100%) and most or all hybrid individuals had alien alleles at only one or a few of six unlinked diagnostic loci, indicating that post-F 1 hybrids represent the majority of individuals in these stocks and introgression has taken place. Release or escape of introgressed individuals from hatcheries into natural water bodies should be avoided in order to protect the biological diversity and genetic integrity of native fish populations. Key words: Diagnostic loci, Hybridization, Hybrid swarm, Microsatellites, mtDNA, nDNA Introduction Arctic charr, Salvelinus alpinus has an Holarctic distribution and shows the highest phenotypic plasticity among all charrs. Landlocked and anadromous or dwarf and normal forms occupying several different feeding niches with