Polyploidization is a widespread and important process in the plant evolution and in individual plant development. Polyploids are used in plant breeding programs for improving different crop varieties. Genome spontaneously becomes autoplyploid via chromosomal nondisjunction in mitosis or meiosis, endoreduplication, cell fusion or inhibition of cytokinesis. Polyploids also occur among regenerated plants from in vitro culture or during transformation process. Comparative molecular and cytogenetic genome investigations have revealed that many plant species recognised as diploids are in fact polyploids. Molecular cytogenetics methods, especially genomic in situ hybridization (GISH), allow for distinguishing ancestral genomes and chromosomal rearrangements appearing in the course of evolution or/and biotechnological manipulations.