A major emphasis in breeding for iron toxicity tolerance in rice is to identify differences that are associated with resistance and harness them for genetic improvement. In this study, thirty accessions, including IRRI gene bank accessions, two varieties from Brazil, 8 cultivars from West Africa and 10 cultivars from Uganda were analyzed for sensitivity to iron toxicity, and genetic diversity using morphological and SSR markers. Two genotypes, IR61612-313-16-2-2-1 and Suakoko 8 showed significantly high resistance with an average score of ${leq}3.5$ on 1 - 9 scale. The SRR markers were highly informative and showed mean polymorphism information content (pic) of 0.68. The PIC values revealed that RM10793, RM3412, RM333, RM562, RM13628, RM310, RM5749, and RM154 could be the best markers for genetic diversity estimation of these rice cultivars. Diversity at the gene level showed an average of 4.61 alleles ranging from 2 to 12 per locus. Mean gene diversity (H) value for all SSR loci for the 30 genotypes evaluated was 0.69 but was decreased to 0.53 when analysis was performed on Ugandan accessions. The low genetic diversity found among the Ugandan accessions is the evidence of a narrow genetic base, and such a scenario has a potential vulnerability for resistance break down. A low correlation was detected between the observed molecular and morphological datasets. This means that a combination of morphological traits and SSR analysis would be required when assessing genetic variation under iron toxic conditions, and could be a practical strategy for breeders when planning crosses. A distinction between the resistant and susceptible accessions in both phenotyping and SSR datasets suggests the presence of unique alleles that could be harnessed for improvement of rice against iron toxicity.