Unrelated families of repetitive DNA were identified in the genome of Atlantic salmon (Salmo salar) and characterized. -- 1) A segment of DNA containing a single Bg/I repeat tandem array was isolated from a genomic library. Bg/I repeats comprise 2.3% of the S, salar genome and were found in the vicinity of rDNA genes. Southern blot hybridization detects a homologue of the Atlantic salmon Bg/I repeat in the brown trout (Salmo truita) genome but not in other salmonids. However, a DNA fragment with sequence homology to part of the Bg/I repeat has been isolated from Arctic charr (Hartley and Davidson 1994). The Bg/I repeat also detects RFLPs in Atlantic salmon. -- 2) Tel transposon-like sequences are present in salmon, trout, and charr species and may belong to several families that do not follow phylogenetic lines. As many as 15,000 copies reside in the Atlantic salmon haploid genome. The complete DNA sequence of one transposon-like element (SALT1) in Atlantic salmon is 1535 base pairs long. It contains terminal inverted repeats and a degenerate open reading frame of 1273 nucleotides whose inferred amino acid sequence shares homology with transposases from Caenorhabditis sp. and Drosophila sp. Zoo blot analysis indicates that Tel transposon-like sequences are present in other lower vertebrates including several fish species and amphibians but the copy number can vary significantly in different lineages. -- 3) Members of the NheI family share a great deal of sequence similarity with one another and with corresponding elements present in brown trout (over 95% identity). These elements, which comprise more than 1.2% of the Atlantic salmon genome, do not exist in long tandem arrays as is typical of satellite DNA. Subfamily structure exists and there is evidence that members of the same subfamilies are found in both Salmo species. Sequences homologous to the NheI repeat are located within a 1424-bp segment inserted immediately downstream of the 5' end of a Tc1 transposon-like sequence isolated from Atlantic salmon (Radice et al. 1994). -- 4) Various minisatellite and other short tandem repeat loci were characterized. Southern blot analysis of the phylogenetic distribution of a subset of the minisatellites indicates one sequence to be pervasive among vertebrates, others present only in Salmoninae or Salmonidae species, and one selectively amplified in Atlantic salmon. Their value as probes for detecting variable number tandem repeat loci is assessed. Evidence exists for coevolution of microsatellite and minisatellite arrays at some loci.