This study revealed the historical interactions between various regions of Japan and Palau by comparing banana cultivars using DNA analysis. Since domesticated banana cultivars have vegetative reproduction characteristics, identifying these cultivars and constructing a phylogenetic tree would provide an understanding of human interactions. Consequently, morphological classification and interviews on local names, origins, and usage patterns were conducted by referring to historical documents to interpret the phylogenetic tree. From the 19th century onward, the results showed a close interaction among Ogasawara Islands, Hachijo, Ryukyu Islands, and Palau, which are historically included in/excluded from “Japan” and geographically considered as a part of Oceania. Therefore, the analysis of banana cultivars is an effective method for clarifying the regional history and exploring the origins of agriculture in Oceania and Asia.