Genome diploidization following WGDs can proceed with different intensities and be accompanied by speciation events. However, it remains unclear how and to what extent chromosomal diploidization is associated with more fine-scaled genomic diploidization. Genomes of the Microlepidieae species (Brassicaceae), endemic to Australia and New Zealand, originated after an ancient allotetraploidization event and subsequently evolved into different species and subclades with distinct levels of inter-subgenome reshuffling and descending dysploidy. Here, we sequenced genomes of Microlepidieae and related species with different karyotypes and genome sizes. Large structural differences underlying karyotype evolution were consistently supported by both sequencing-based and molecular cytogenetic results. The expansion of genome size was mainly caused by the accumulation of LTR retrotransposons, especially Athila elements. We identified genomic regions corresponding to two subgenomes based on different gene fractionation and gene tree topologies, and shared karyotype structures with closely related diploid genomes. Our genomic evidence confirms the most likely Asian origin of the allotetraploid ancestral genome. Whereas the maternal subgenome with an n = 8 genome structure conserved within the Camelinodae supertribe is sister to the Crucihimalayeae tribe, the paternal subgenome had an n = 6 karyotype identical to the extant genomes of the Yinshanieae tribe. In Australia, descendant genomes of the allotetraploid ancestor (n = 14) exhibited different extent of gene loss/pseudogenization between subclades, consistent with the previous cytogenetic observation of two-speed diploidization. Our results provide new insight into the process of post-polyploid genome evolution in plants. We acknowledge the support of the Czech Science Foundation (20-03419Y).