Integrative morphological and multilocus molecular analysis reveals intraspecific genetic structuring in Anoectochilus roxburghii (Orchidaceae) from central Vietnam

Anoectochilus is a high-value medicinal orchid threatened by overexploitation and habitat degradation. However, integrated micro-morphological and molecular data for natural Vietnamese populations remain limited. This study provided a comprehensive characterisation of 17 accessions collected from Bach Ma National Park using detailed micro-anatomical analysis, multi-locus DNA barcoding ( ITS , rbcL , psbA-trnH ), and SSR-based genetic profiling. Micro-morphological assessment revealed substantial intra-population differences. Additionally, correlations between anatomical traits and vegetative growth parameters suggested structural contributions to phenotypic variability. DNA barcoding confirmed species identity, Anoectochilus roxburghii , with high similarity (98.92–100%) to reference sequences. Among the tested barcode loci, ITS exhibited the highest discriminatory power. Despite low nucleotide diversity in barcode regions, SSR analysis detected moderate-to-high polymorphism (He ≥ 0.408; PIC ≥ 0.327) and resolved the population into four genetic clusters with similarity coefficients ranging from 0.39 to 0.93. This contrast between barcode homogeneity and SSR diversity showed the evolutionary process within the population. Moreover, these findings could establish a good baseline for conservation management and future marker-assisted breeding of A. roxburghii .