Two related satellite DNA families (satellite I and satellite II) with complex higher-order repeat (HOR) monomers represent major DNA components equilocated in the pericentromeric heterochromatin of all Tribolium madens chromosomes. Fragments obtained upon genomic DNA restriction revealed two subfamilies of satellite II monomers, and also identified regions of transition between satellite I and satellite II sequences. The two subfamilies differ not only in diagnostic nucleotides, but also in flipped orientation of constituent subunits. Hybrid genomic fragments comprise directly linked satellite I and satellite II monomers that cannot be distinguished from randomly cloned monomers of corresponding families. An exception is the most proximal satellite I monomer in the hybrid fragment named TMADhinf, which shows sequence divergence typical for repeats evolving at array ends, in zones of low homogenization efficiency. This pattern points to the extensive rearrangement processes generating abrupt transitions between satellite arrays combined with array maintenance by unequal crossover. Switching points between adjacent satellites as well as the edges of flipped subunits are localized within a short sequence segment, indicating a preferential site of recombination within satellite subunits. Multiple copies of TMADhinf junction fragment support the hypothesis that sites of evolutionary origin of novel satellite repeat (sub)families can be localized at array ends, in regions of enhanced sequence divergence.