Chickpea (Cicer arietinum
L.) is one of the main sources of plant proteins in the Indian subcontinent and West Asia, where two different morphotypes are grown. Here, we developed a system for fast molecular karyotyping for both morphotypes of cultivated chickpea by oligo-fluorescence in situ
hybridization (FISH) barcodes. Our results show the potential of oligo-FISH barcoding for the identification of structural changes in chromosomes, and pointed out some problematic, most probably wrongly assembled regions of the pseudomolecules of both kabuli and desi reference genomes.