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Here, we used double-digest restriction site-associated DNA sequencing to assess genetic diversity, population structure and demographic history in Amomum hainanense, and assembled complete chloroplast genomes from low-coverage whole-genome sequencing reads to clarify its phylogenetic placement. Genome-wide single nucleotide polymorphisms revealed exceptionally low nucleotide diversity (\u03c0 = 0.7\u20131.7 \u00d7 10\u22124 among the five well-sampled populations; mean = 1.2 \u00d7 10\u22124), substantially lower than values reported for cultivated source taxa of Amomi Fructus (4.1\u201310.4 \u00d7 10\u22124). Pronounced population structure and high, statistically significant pairwise genetic differentiation (FST = 0.280\u20130.621) were consistent with restricted connectivity among populations. Stairway Plot 2 based on both pooled and principal component analysis-defined group-level folded site frequency spectra recovered a broadly consistent long-term decline in effective population size over the last ca. 10 000\u2005years. Chloroplast genomes showed very low intraspecific diversity (\u03c0 \u2248 0.2 \u00d7 10\u22124) and recovered A. hainanense as a strongly supported monophyletic lineage. Phylogenetic analysis of three plastid loci further identified A. repoeense as the closest sampled relative. Together, these results indicate severe genetic erosion coupled with strong population subdivision in A. hainanense. We recommend prioritizing in situ protection of the highest-diversity populations (XL and MLD) and establishing population-stratified ex situ germplasm collections that represent all major genetic groups.<\/jats:p>","DOI":"10.1093\/aobpla\/plag045","type":"journal-article","created":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T11:59:04Z","timestamp":1790164744000},"source":"Crossref","is-referenced-by-count":0,"title":["Genomic evidence for genetic erosion and strong population subdivision in\n                    <i>Amomum hainanense<\/i>\n                    (Zingiberaceae), an endangered island endemic plant from Hainan, China"],"prefix":"10.1093","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0009-0005-7652-3603","authenticated-orcid":false,"given":"Liang","family":"Tang","sequence":"first","affiliation":[{"name":"Hainan Baoting Tropical Forest Ecosystem Observation and Research Station, School of Ecology, Hainan University , 58 Renmin Avenue, Haikou 570228, Hainan ,","place":["China"]},{"name":"International Joint Center for Terrestrial Biodiversity Around South China Sea of Hainan Province, School of Ecology, Hainan University , 58 Renmin Avenue, Haikou 570228, Hainan ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xu","family":"Wu","sequence":"additional","affiliation":[{"name":"Hainan Baoting Tropical Forest Ecosystem Observation and Research Station, School of Ecology, Hainan University , 58 Renmin Avenue, Haikou 570228, Hainan ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi-ting","family":"Xu","sequence":"additional","affiliation":[{"name":"Hainan Baoting Tropical Forest Ecosystem Observation and Research Station, School of Ecology, Hainan University , 58 Renmin Avenue, Haikou 570228, Hainan ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lang-xing","family":"Yuan","sequence":"additional","affiliation":[{"name":"Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences , No. 4 Xueyuan Road, Longhua District, Haikou 571101, Hainan ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-4491-0186","authenticated-orcid":false,"given":"Lian","family":"Zhou","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences , No. 20 Nanxincun, Xiangshan, Beijing 100093 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shou-bai","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Tropical Agriculture and Forestry, Hainan University , 58 Renmin Avenue, Haikou 570228, Hainan 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