Summary Micronuclei are extra nuclear structures, formed by the exclusion of chromosomes during cell division. The genotoxicity of a compound and its impact on the genome can be assessed via micronuclei formation. The present study has been undertaken to evaluate the mutagenic effect of the alkylating agent EMS on the meiotic behavior of pollen mother cells of Phaseolus vulgaris L. The cytological analysis revealed the induction of micronuclei at all the three administered concentrations of EMS, viz. 0.1, 0.3 and 0.5%. Besides micronuclei formation, other meiotic abnormalities associated with chromosomal segregation, such as stickiness, laggard, bridge, multivalent, etc., were also reported at metaphase I/II and anaphase I/II. The micronuclei formed would have two fates either it remains until the tetrad stage or is expelled out in the form of microcytes which will give rise to sterile pollen grains affecting the pollen fertility. The present study also documents the first instance of nuclear budding in Phaseolus vulgaris L. It is contemplated that these nuclear buds will later on convert into micronuclei. The micronuclei formation results in partial elimination of the genome, which could be efficiently utilized in breeding programmes for the production of addition and substitution lines. Similarly, haploid lines could also be produced by the complete loss of genome. It is therefore essential to understand the biological aspects of micronuclei formation, its consequences on the cell carrying it and other factors related to it so that in the future, it could be used as a marker of genetic damage and also be utilized in breeding programmes.