False smut caused by Ustilaginoidea virens is an emerging disease of rice in India. The disease is causing economic loss to farmers through the reduction of yield and quality of rice. To devise a suitable approach to manage the disease effectively, an understanding of the genetic diversity and population structure of the pathogen is essential. Hence, a total of 34 isolates of U. virens obtained from different locations in India were characterized using 25 genomes-specific SSR markers showing higher polymorphic information content (PIC) that produced 203 alleles with a mean of 8.12 per marker. The genetic diversity varied from 0.00 to 0.885 with an average of 0.673. Based on the phylogenetic tree, the 34 isolates of U. virens were grouped into two major clusters (Cluster I and Cluster II). Cluster I included isolates from Andhra Pradesh, Bihar, Kerala, Manipur, Mizoram, Punjab, and West Bengal, while Cluster II included isolates from Assam, Manipur, Meghalaya, and Odisha. The isolates from the same/nearby locations were partially assembled into the same cluster. The analysis of molecular variance (AMOVA) showed the highest variation of 86% found among the individuals while the least variation of 14% was observed between the populations. The population structures of 34 isolates of U. virens evaluated using STRUCTURE and Principal coordinates analysis (PCoA) separated the 34 isolates into two distinct subpopulations. The high genetic variation in the isolates indicated their substantial potential to evolve and mutate, potentially causing damage to rice crops in future.