Repetitive DNAs are key drivers of genome evolution, but their dynamics accompanying divergence of Aegilops genomes remain incompletely understood. Tandem repeats often serve as FISH markers in phylogenetic studies, however, few families have been used for evaluating relationships among Aegilops species. In this study, we employed three recently discovered satellite repeats, pTa-713, pTa-566 and oligo-45, to analyze diploid Aegilops taxa to gain a deeper insight into the chromosomal mechanisms of genome evolution. We analyzed 121 accessions representing 11 diploid Aegilops species using these three probes and showed that they are effective for chromosome and genome identification in Aegilops. For each species, we established a generalized karyotype and assessed intra- and interspecific polymorphisms. Diploid genomes varied in repeat content and distribution; Ae. speltoides had the highest pTa-713 content, whereas D-, M- and N-genomes were highly abundant in oligo-45. The specific labelling patterns allowed us to subdivide Aegilops into six groups, mostly consistent with the taxonomic classification of the genus. FISH results showed that Ae. tauschii is karyotypically highly distinct from species of the Sitopsis group, which contradicts topologies established via the analysis of low-copy DNA sequences, likely due to different evolutionary pathways between coding- and non-coding DNA fractions.