Early seedling vigour (ESV) is an important trait for early establishment of rice crop in the direct seeded condition. In the present study, genetic diversity in a set of 91 rice accessions of improved varieties, landraces and wild rice accessions of Oryza nivara and Oryza rufipogon were assessed by 52 microsatellite markers associated with early seedling vigour QTLs. A total of 82 alleles were amplified with an average of 2.34 alleles per locus and their PIC values ranged from 0.374 to 0.071 with an average of 0.33. The model based population structure approach grouped the total rice accession into two distinct populations ranged between 0.104 (population 1) and 0.334 (population 2), while allele frequency divergence between two populations was 0.105. The phylogenetic analysis grouped the genotypes into five major clusters and 12 sub-clusters. Results indicated that, these rice genotypes exhibited a high genetic diversity and could be useful in rice improvement programme specific to ESV.