Sweetpotato is a globally important crop with numerous wild relatives harboring extensive genetic diversity. In this study， a comparative genomic analysis was conducted using two publicly available high-quality genomes of wild relatives. Our analysis identified 1798184 genome-wide single nucleotide polymorphisms （SNPs）， along with 2076 translocations and 84 inversions encompassing 2106 genes. Enrichment analysis showed that these genes are mainly enriched in pathways such as the biosynthesis of secondary metabolites. Among them， the breakpoints of 34 inversions are located inside the genes and may affect the structure of these genes. There are 10226 insertion-type and 11411 deletion-type structural variations between the two genomes. We annotated these structural variations and conducted gene enrichment analysis on those structural variations that may affect gene function or expression. We found that these potentially affected genes were mainly enriched in pathways of secondary metabolites， while genes related to functions such as DNA repair and replication were enriched. Through deploying statistical results of the synonymous substitution rate （Ks） and fourfold degenerate synonymous site （4DTv） of collinear gene pairs of two wild species and other related species， it was indicated that the common ancestor of the genus Ipomoea differentiated into different species after a whole-genome triplication event. Collectively， the findings will provide insights for the excavation of excellent variations in wild relatives of sweetpotato as well as for analyzing species differentiation