The establishment ofArabidopsisas the most important plant model has also brought other crucifer species into the spotlight of comparative research. While the genusCapsellahas become a prominent crucifer model system, its closest relative has been overlooked. The unispecific genusCatolobusis native to temperate Eurasian woodlands, from eastern Europe to the Russian Far East. Here, we analyzed chromosome number, genome structure, intraspecific genetic variation, and habitat suitability ofCatolobus pendulusthroughout its range. Unexpectedly, all analyzed populations were hypotetraploid (2n= 30, ~330 Mb). Comparative cytogenomic analysis revealed that theCatolobusgenome arose by a whole-genome duplication in a diploid genome resembling Ancestral Crucifer Karyotype (ACK,n= 8). In contrast to the much youngerCapsellaallotetraploid genomes, the presumably autotetraploidCatolobusgenome (2n= 32) arose early after theCatolobus/Capselladivergence. Since its origin, the tetraploidCatolobusgenome has undergone chromosomal rediploidization, including a reduction in chromosome number from 2n= 32 to 2n= 30. Diploidization occurred through end-to-end chromosome fusion and other chromosomal rearrangements affecting a total of six of 16 ancestral chromosomes. The hypotetraploidCatolobuscytotype expanded toward its present range, accompanied by some longitudinal genetic differentiation. The sister relationship betweenCatolobusandCapsellaallows comparative studies of tetraploid genomes of contrasting ages and different degrees of genome diploidization.