Knowledge of rice genetic diversity is necessary to ascertain the germplasm conservation and the development of improved rice genotypes with good quality traits through various breeding programs. The aim of this study was to determine the genetic diversity based on gel consistency and alkali digestion among selected Kenyan and Tanzanian genotypes using SSR markers. PowerMarker version 3.25, GenAlEx version 6.41 and DARwin 6.0.12 statistical software were used to carry out data analysis. The number of alleles per locus ranged from 2 to 4 with an average of 2.75 across the 8 markers used. Polymorphic information content (PIC) ranged from 0.5224 (RM577) to 0.1411 (RM85) with an average of 0.3673 observed across all the markers. Gene diversity ranged from 0.5764 (RM577) to 0.1528 (RM85) with an average of 0.4181 with one rare allele was detected at RM577 loci. Pairwise genetic dissimilarity matrix ranged from ranged from 0.9333 to 0.1818 with the least genetic distance being observed between IR 54 and BS 370 while the highest, 0.9333 being between Saro 5 and IR 2793. The unweighted neighbour joining tree clustered the rice genotypes into three major clusters and subsequent sub clusters hence effectively differentiating the Kenyan and Tanzanian genotypes based on gel consistency and alkali digestion. This clustering was complemented with the findings in the principal coordinate analysis. These results show that determination of genetic diversity using SSR markers cam be successfully achieved. In this study RM577 was the best and most informative SSR marker given it showed the highest PIC, gene diversity and allele per locus. In addition, it's the only marker that showed a rare allele at 400 bp.