Leptestheria dahalacensis genome harbours repeats of the LEP150 satellite DNA family linked to 5S gene, within the ribosomal intergenic spacer. In genetically isolated samples, the sequence analysis of the region (5S, flanking region, first satellite monomer: unit A, second satellite monomer: unit B) evidenced three 5S variants. The alpha and gamma variants share a greater homology. They co-occur in the Central European samples, while in the Italian one, the highly divergent alpha and beta variants are present. In phylogenetic analyses, A and B LEP150 monomers show a peculiar clustering; this was further confirmed through the sequencing for the alpha variant of four monomers at the 5' and 3' tails (units A, B, C, D and D', C', B', A', respectively). Horizontal homogenisation was observed only across C, D, C' and D' units. Furthermore, repeat sequence diversity decrease toward terminal repeats, at variance of literature data. The pattern of variation observed is explained taking into account the presence at the LEP150 array borders of two loci under natural selection: the 5S rRNA gene, upstream, and the rDNA transcription promoter, downstream. These elements may drive the dynamics of flanking regions and linked repeats in a process similar to selective sweep. At variance of classical genetic hitchhiking, the selective sweep here scored should be realized and maintained through an interplay of selection and molecular drive.