Cytological analysis of EMS (Ethyl methane sulphonate) treated population of Fagopyrum esculentum revealed an abnormal behaviour of microsporogenesis that affected the meiotic events resulting in the formation of abnormal meiotic products that prevent the gamete formation and impair pollen fertility. The two desynaptic mutants were recorded, showing distinctive variations in the morphology as compared to the control plants. The seeds of Fagopyrum esculentum were treated with EMS solution in different concentrations such as 0.1, 0.3 and 0.5% using potassium phosphate buffer (pH 7) for 5 h. During cytological investigation, 0.5% concentration of EMS enhanced the univalent frequency per cell at diakinesis/Metaphase I, respectively along with unequal segregation at anaphase I which is pronounced to be higher in contrast to bivalents. Because of higher frequency of univalents desynapsis has been categorized as medium-strong type. EMS induced desynaptic plants showed abnormal meiotic behaviour leading to pollen sterility and no seed setting was recorded. The chemical mutagen has acted on recombination genes system which is accountable for synapsis and chiasma formation and further disrupted the complete chiasma assembly. The desynaptic mutant is a potential tool that provides genetic information on the maintenance of chiasma and the study offers the possibility for formation of aneuploids production which may be exploited successfully through chemical mutagenesis in breeding programmes.