Land races adapted to a variety of agro-ecological niches constitute a rich source of rice biodiversity. Large-scale cultivation of high-yielding varieties has resulted in the replacement of the land races, except a few that are still being cultivated by the resource-poor farmers practising subsistence farming. From the viewpoints of their conservation and utilization, it is important to understand the genetic structure of the present-day land races. The present study was designed to explore if the present-day land races of rice still retain a composite genetic structure that forms the basis of their stability. Two land races, which are being grown by the rural farmers in the coastal regions of Orissa over several generations, were characterized and compared with four commercial high-yielding varieties using sequence-tagged microsatellite site (STMS) markers. A high-resolution (3% Metaphor) agarose gel when compared with 6% denaturing PAGE was found useful for the differentiation of the STMS alleles. The DNA profiles based on forty-eight mapped STMS markers revealed a high degree of genetic diversity between the land races and the commercial varieties. Analysis of 18 individual plants of each land race and variety, using ten most informative markers detected a high degree of genetic uniformity in the commercial varieties. Residual heterozygosity for only one of the marker loci was evident in the case of the popular commercial cultivar, Lalat. In both the land races, heterozygosity and heterogeneity were clearly evident with the presence of additional marker locus genotypes carrying new STMS alleles at much lower frequency than the major allele. Of the two land races characterized, one (Galleiganthi) was more heterogeneous than the other (Bankosa).