The genus Aubrieta Adan. (Brassicaceae) is widely distributed and diverges across different elevations. We aimed to study aspects of the genome organization and components to understand evolution and differentiation. Endogenous pararetroviruses (EPRVs) were examined in whole-genome of four Aubrieta species using high-throughput DNA sequencing and bioinformatics. Two genera of caulimovirid sequences have been found in the four examined genomes, caulimoviruses, and florendoviruses with four members each named as Caulimovirus-AAn, Caulimovirus-AEu, CaulimovirusAGr, Caulimovirus-ASc, AanaV, AeurV, AgraV, and AscaV. The full length of CaulimovirusAAn, Caulimovirus-AEu, Caulimovirus-AGr, and Caulimovirus-ASc were 7579, 6726, 7223, and 6609 bp, while the florendoviruses, AanaV, AeurV, AgraV, and AscaV were 6675, 6888, 6702, and 6638 bp respectively. The integrants encode four coding domains; movement protein (MP), two domains of reverse transcriptase (RT and RVT), and RNaseH (RH), and except Caulimovirus- AEu, all caulimoviruses are inverted from 3' to 5', while the florendoviruses are arranged from 5' to 3'. Variable numbers of genome proportions and copies have been recorded for these integrants reporting A. eurobsens as more accessible genome in the case of florendoviruses, while caulimovirus-like sequence was most abundant in the genome of the A. anamasica. The genome of A. scardica was limited in EPRVs existence comparing to A. anamasica which having a good marker to separate these species. The phylogenetic tree confirms the close relationships of each group of the EPRVs as they are arranged next to their genus members.