Synaptic mutants are the subject of a special concern to cytologists and geneticists as they hold the variability in their recombination pattern. Seeds of Trachyspermum ammi (L.) Sprague (ajwain) were treated with Ethyl Methane Sulphonate (EMS) solution at 3 different concentrations viz. 0.1%, 0.3% and 0.5% for 5 h, prepared in potassium phosphate buffer with 7.0 pH. During meiotic observation of 0.3% concentration of EMS treated population of ajwain, the Pollen Mother Cells (PMCs) of the two plants showed a desynaptic behavior with a high frequency of a univalent formation along with a few bivalents at diakinesis/metaphase I. Apparently, EMS might be involved in the formation of substandard synaptic proteins which reduced the chiasma formation, suggesting that EMS has the ability to generate the male sterile lines. Along with the univalent formation, other various chromosomal aberrations were also analyzed in the subsequent stages of meiotic division viz. laggards, bridges, unequal separation, and disturbed polarity with abnormal tetrads. Thus, both the desynaptic plants displayed a high incidence of pollen sterility. The present investigation made an attempt to understand the meiotic behavior of desynapsis and its consequences on the pollen fertility of the ajwain crop.