The species of Akebia Decne are well-known medicinal plants and have been used in Chinese herbalism for at least 2000years. The Akebia fruits have a delicious flavor and high nutritional value and are especially rich in antineoplastic, diuretic and antiphlogistic properties, making them worthy of being exploited as a new high-value crop. However, the nature habitats of the Akebia species have been fragmented due to rapid and intensive expansion of agricultural land. In this study, population genetics based on simple sequence repeat markers were conducted on the three most economically important Akebia species in order to reveal the genetic effects of habitat fragmentation to gain useful information for conservation and management of genetic resources of Akebia. Three Akebia species maintained high within-population genetic variation and low level of genetic differentiation. Mantel's test indicated that there was a significantly positive correlation between genetic distance and geographic distance. Our results reveal the resilience of genetic diversity within extant populations of three Akebia species to chronic forest fragmentation. For breeding purpose, germplasm collection for sampling as many individuals as possible from many populations to maximize genetic diversity of the species is recommended. In addition, natural introgression events have been revealed by Cluster and Structure analysis where admixed ancestry occurred across three marginal populations of A. trifoliata ssp. australis, suggesting these populations should be given priority for germplasm collection.