This study examined Ethiopian yam genetic diversity and population structure using SSR markers. Ten SSR markers were used to analyze a total of 118 yam genotypes representing six population species that were collected from four zones in western Ethiopia. A total of 92 alleles with an overall mean of 9.2 per locus were detected. The average expected heterozygosity (He) and allelic richness (AR) were 0.88 and 6.30, respectively. All SSR markers were polymorphic and highly informative, with an overall mean polymorphic information content (PIC) of 0.87. More ever, all SSR markers discriminated the variations among the studied yam species. The overall mean expected heterozygosity (He) and percentage of polymorphic loci within populations were 0.72 and 98.33, respectively. The highest genetic diversity indices were recorded in the landrace yam populations of D. cayenensis, D. bulbifera, and D. rotundata species. Analysis of molecular variance (AMOVA) revealed a moderate but highly significant genetic differentiation (PhiPT=0.100, p <0.0001). Most of the total genetic variation (91%) accounted for the within-population variation, leaving only 9% for the among-population genetic variation. STRUCTURE analysis based on the Bayesian model weakly inferred two subgroups (K=2), confirming the high potential of genetic admixtures and close relationships among the studied yam genotypes, likely due to the presence of high gene flow (Nm= 2.39). D. alata landraces had the least genetic diversity, inferring the need for strong conservation strategies. This study provided baseline genetic diversity data for yam breeders to selectively breed for desirable agronomic qualities and devise conservation measures.