Sweetpotato, Ipomoea batatas(L.) Lam., is an important food crop widely cultivated in the world. Evaluation of genetic relationships among diverse cultivars and landraces is necessary for efficient exploitation of genetic diversity in the existing germplasm resources. In the present study, a collection of 380 sweetpotato accessions assembled from different agro-climatic zones of China and other countries were genotyped using 30 SSR primer pairs. Model-based structure analysis separated the germplasm into three populations, P1, P2 and P3, containing 228, 133 and 19 accessions, respectively, which was consistent with the results of phylogenic and principal component analysis(PCA). Analysis of molecular variance(AMOVA) revealed significant genetic differentiation among inferred populations, accounting for 16.47% of the total molecular variance, however, the differences between the regions were not significant, the total variation were due to the differences between the genotypes within the population. Pairwise fixation index(F ST) suggested that populations P1 and P3 had the highest differentiation, while populations P1 and P2 had the lowest differentiation. The diversity among populations was wide, which confirmed the genetic distinction of populations. Through comparing model-based structure and domestication-based classification, it was found that the accessions of population P1 mainly belonged to modern cultivars, and the accessions of populations P2 and P3 basically corresponded to landraces, by which we suggest that modern cultivars maybe had experienced a two-step domestication history. Our results illustrated clear genetic relationships among 380 sweetpotato accessions, exhibiting the potential of accelerating the process of future sweetpotato breeding program by molecular marker based parental selection. Sweetpotato, Ipomoea batatas (L.) Lam., Is an important food crop widely cultivated in the world. Evaluation of genetic relationships among diverse cultivars and landraces is necessary for efficient exploitation of genetic diversity in the existing germplasm resources. In the present study, a collection of 380 sweetpotato accessions assembled from different agro-climatic zones of China and other countries were genotyped using 30 SSR primer pairs. Model-based structure analysis separated the germplasm into three populations, P1, P2 and P3, containing 228, 133 and 19 accessions, respectively, respectively, which were consistent with the results of phylogenic and principal component analysis (PCA). Analysis of molecular variance (AMOVA) revealed significant genetic differentiation among inferred populations, accounting for 16.47% of the total molecular variance, however, the differences between the regions were not significant, the total variation were due to the differences between the genotypes within th e population. Pairwise fixation index (F ST) suggested that populations P1 and P3 had the highest differentiation, while populations P1 and P2 had the lowest differentiation. The diversity among populations was wide, which confirmed the genetic distinction of populations. Through comparing model- based structure and domestication-based classification, it was found that the accessions of population P1 it belonged to modern cultivars, and the accessions of populations P2 and P3 represented corresponded to landraces, by which we suggest that modern cultivars maybe had experienced a two-step domestication history. Our results illustrated clear genetic relationships among 380 sweetpotato accessions, exhibiting the potential of accelerating the process of future sweetpotato breeding program by molecular marker based parental selection.