Abstract: The genetic relationship and distance among rice varieties widely being used as parents by the African Rice Center (WARDA) are largely unknown but of great interest for breeding programs. The genetic relationship among 16 rice varieties was investigated using 83 EST and 174 SSR markers. Similarity among the 16 varieties varied from 21.9 to 91.2% for SSRs and 30.9 to 98.8% for ESTs. The extent of similarity of the four NERICA`s with their donor (CG 14) and recurrent (WAB 56-104) parents ranged from 26.8 to 46.8% and 80.4 to 92.7%, respectively. Genetic similarity within the four NERICAs was the lowest between NERICA 1 and NERICA 6 (76.7 to 86.4%), which is in agreement with differences in agronomic traits. Cluster and principal component analyses performed on both marker types revealed three major groups for the cultivated rice species: the glaberrima group, indica group and NERICA and japonica group. The wild species, O. longistaminata, appeared to be close to the glaberrima than the other groups. Sixty four markers (22 EST and 42 SSR) were sufficient to clearly separate the 16 varieties into their respective group. Matrices correspondence tests demonstrated the presence of greater correspondence between the phenograms derived from SSRs and ESTs (r = 0.96).