A bacterial artificial chromosome (BAC) library constructed from the short arm of rye (Secale cereale L. ) chromosome 1R has been screened for clones containing copies of the pSc200 tandem repeat family, most abundant in rye subtelomeric heterochromatin. The molecular organization of the monomer array and adjacent sequences has been studied in BAC 126/C20. Digestion of the array with various restriction endonucleases reveals no higher-order organization. The DNA adjacent to the pSc200 array consists of different repeats, including retrotransposon derivatives and another tandemly repeated family, termed XbaI, with a monomer length of 576 bp, 475 of which show 82% similarity to the long terminal repeat of the known Cereba retrotransposon. Sequencing of the 13 kb long genomic region in BAC 126/C20 revealed a direct junction of the pSc200 and XbaI monomers. The arrays of both families terminate at the same AT-rich sequence САААААТ. Another recombination signal is the presence of palindromes in the close proximity to the junction site. The presence of microhomologies promotes the action of proteins involved in double-strand DNA break repair. To our knowledge, it is the first discovery of the direct junction of monomers that are longer than 100 bp and belong to different families of plant tandem repeats.