Sweetpotato [Ipomoea batatas (L.) Lam] breeding is important for food security and health in East Africa (EA), and a breeding platform in Uganda provides national researchers and breeders in EA with true seed. Our objectives were to characterize genetic relationships among parental material used at the EA breeding platform. There were 135 parents and six check clones analyzed using 31 simple sequence repeat primers. An average of 7.13 alleles per primer was found, and Jaccard similarity coefficients were in the range of 0.298 to 1.00 with a mean of 0.542. Unweighted pair group cluster analysis placed most African parents in two main subclusters showing no association with morphology or geographical origin. The subclusters were also supported by principal coordinate analysis, derivative analysis of principal components, and population structure simulations. The analyzed breeding material from EA was highly genetically variable, grouped in two distinct genetic pools, and suitable to study heterosis exploiting breeding schemes.