The high percentage of hybrid species and interspecific hybrids in plants and a large number of genes in com-parison with animals shows that hybridization played a major role in plant taxonogenesis. The article shows that the data of comparative genomics have revealed the genetic mechanisms of processes observed at different stages of plant speciation in the cases where it goes through events of distant (interspecific) hybridization, often accompanied by polyploidization. Fast and long-term consequences of these processes are considered. Distant hybridization is accompanied by the highest possible genomic, repeatomic, transcriptomic, pro-teomic, metabolomic and phenomic variety. Transposons and microRNA are important factors in genome and phenotype variability after distant hybridization. Some mechanisms of transposons actions and their manifestation at the level of morphological features are described. In the history of all plant taxa, appar-ently, the following cycle repeatedly took place: interspecific hybridization – polyploidization – genomic shock – burst of genome and transcriptom variability induced by transposons – “domestication” of new transposons, loss of part of paralog genes, acquisition of new functions by some of duplicated genes – karyotype stabilization – secondary diploidization. All this is consistent with “Hegelian triad”, on which V.L. Komarov was pondering.