Owing to a long history of rice cultivation and a rice improvement programme, Sri Lanka is home to a diverse range of rice germplasm. Characterization of germplasm is essential to provide information to the final users for the maximum utilization of a germplasm collection. Therefore, this study was carried out to assess the genetic diversity of rice (Oryza sativa L.) using seed storage proteins as a fingerprinting tool. A total of thirty two rice varieties including both traditional and newly improved varieties were subjected to seed protein extraction, followed by denatured-sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and silver staining. Resultant gel showed a total of twelve bands consisting of four monomorphic and eight polymorphic bands. Protein quantification using Gel Quant.NET 1.6.6 software revealed the highest and the lowest protein levels in BW 272-6b and BG 360 respectively. Dendrogram obtained from both protein quantification and band binary scoring of SDS-PAGE profile clustered the seed storage protein-rich rice genotypes BW 272-6B, Pachchaperumal, Hondarawalu and Mawee into one group. A unique protein with a size of about 46 kDa in BW 272-6, could be utilized as a protein molecular marker for its identification. The 133 kDa protein present in BW 272-6B, Pachchaperumal and Hondarawalu could be used as an additional fingerprint in identification of these three varieties that are high in protein content. Therefore, this study suggests the use of protein profiling as a molecular tool for diversity exploration of rice genotypes using seed storage proteins.