Diversity studies are now a key tool in genetic conservation work. The perennial herb genus Hosta showed a complex radiation of numerous species in mountains and riversides around the Shikoku Island, Japan. The purpose of this study was to evaluate trnS-trnG regional genetic structure and the genetic divergence within hosta taxa populations in this area. We sequenced trnS-trnG regional (chloroplast DNA) cpDNA in 81 populations comprising 399 individuals of 11 Hosta taxa collected from Shikoku area. The different numbers of haplotypes were found in different taxon. The divergences of population of Hosta genus and individual taxon were shown in NJ phylogenetic tree. The highest number of haplotypes (14) was found in H. longipes var. gracillima. H. sieboldiana and H. kiyosumiensis populations showed the maximum haplotype diversity (1.0), and H. alismifolia showed maximum nucleotide diversity (π: 0.012). The genetic structures of the H. tardiva with H. kikutii var. caput-avis (FST divergence: 52.7%) and H. sieboldiana with H. tardiva (FST divergence: 52.2%) populations were greatly differentiated from each other (FST value: &gt
0.15 to 0.25). We found maximum evolutionary divergence (0.009) between H. alismifolia and H. kikutii var. polyneuron populations. The significant negative neutrality test values are the evidence of expansion of the total population. H. sieboldiana and H. kiyosumiensis are more widely distributed than other taxa. H. sieboldiana, H. alismifolia, H. longipes var. gracillima and H. kikutii var. polyneuron showed the excessive low frequency variants.