In the present study Isoetes coromandelina ssp. thanensis S.K. Shukla, S.K. Singh, P.K. Shukla, N.K. Dubey, H. Khanam & G.K. Srivastava a micro endemic new subspecies is described from the Than in Rajkot District of Gujarat state in coastal zone of India. Morphologically, the new subspecies is most similar to I. coromandelina ssp. coromandelina but differs in its microspore with levigate surface ornamentation and chromosome number 2n = 22 + 1. Different morphological features of I. coromandelina ssp. thanensis are discussed. Images and a distributional map are also provided. In the present study, we made a correlation between microspore ornamentation and ploidal status at the infra-specific level which helpful in taxonomy of closely related taxa.