<p>Soil salinity significantly limits rice production in Africa, necessitating the development of salt-tolerant varieties. This study evaluated 206 rice genotypes (201 from Eastern and Southern Africa (ESA) and 5 standard checks from IRRI) for seedling-stage salinity tolerance. Thirteen genotypes were further characterized under salinity stress, including eight from ESA and five tolerant and sensitive checks. Salinity reduced both root and shoot dry weights across genotypes. Spearman’s correlation identified sodium content, Na⁺: K⁺ ratio, and leaf temperature at later stress stages as strongly associated with salinity tolerance. Principal component analysis (PCA) revealed that Na⁺: K⁺ ratio, root and shoot dry weights, and shoot length were key contributors to tolerance, accounting for 56.95% of total variation. Based on these traits, genotypes were grouped as tolerant, moderately tolerant, or sensitive. Six genotypes (Intsindagira Bigega, K5, SATO 1, Sukari, Terimbele (LL 29), and ZX 117) showed moderate tolerance and distinct phenotypic traits, making them promising candidates for breeding programs. These moderately tolerant genotypes exhibited distinct characteristics compared to sensitive checks, for example; shoot length, root length, low Na⁺: K⁺ ratio, root dry weight and shoot dry weight. These genotypes could be potential candidates for future breeding programs aimed at enhancing the salinity tolerance of rice varieties. Further research, including comprehensive genotypic screening and field evaluation, is recommended to deepen the understanding of the underlying mechanisms in order to validate the current results for further applications.</p> Graphical abstract <p></p>