ITS-Supported Species Discrimination and ISSR-Based Genetic Diversity and Population Differentiation of Lumnitzera littorea in Southern Vietnam

Lumnitzera littorea is a rare, conservation-relevant mangrove tree with discontinuous records in southern Vietnam, but population-level genetic evidence remains limited. This study combined nuclear rDNA ITS and ISSR markers to distinguish species-level support from population-level comparisons. Can Gio was treated as the focal population, while Dong Nai, Phu Quoc, and Con Dao were used as comparison populations. The 16 study-generated ITS sequences, deposited as PZ348213–PZ348228, supported species-level separation between L. littorea and L. racemosa, with a between-species p-distance of 0.0459 and 32 fixed diagnostic sites across the 697 bp core. The ISSR matrix comprised 115 individuals and 81 loci, and population analyses were restricted to 110 L. littorea individuals. Within this dataset, Dong Nai and Can Gio showed higher ISSR diversity than Con Dao and Phu Quoc. AMOVA indicated significant differentiation among populations (Phi_PT = 0.255, p = 0.001), with 74.5% of variation retained within populations; a mainland–island grouping was also significant (Phi_PT = 0.242, p = 0.001). Repeated n = 20 subsampling retained the relative diversity pattern. The results provide a regional ISSR baseline for conservation-genetics interpretation and support broad representation of local source trees when collecting conservation material; however, they do not define formal management units, official seed-transfer zones, or deep phylogeographic history.