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Abstract Pandanus amaryllifolius, a tropical fragrant screw pine, is commonly used in cooking and traditional medicine. Although studies have analysed its metabolite, transcriptome, and proteome profiles, molecular markers for genetic improvement remain scarce. This study aimed to develop EST-SSR markers from the P. amaryllifolius transcriptome and utilise them to analyse their genetic diversity. We obtained 157,467 unigenes with an average length of 1,084 base pairs. From these, 66,820 EST-SSRs were identified, with dinucleotides being the most common (45.5%). Following functional domain marker (FDM) analysis, 7,208 markers were used for in silico PCR, which revealed 8,843 polymorphic bands (86.9%), with an average polymorphic information content (PIC) of 0.41, gene diversity of 0.54, and a Shannon index of 0.91. The dendrogram and PCA plot clearly separated samples from Malaysia and India. These findings provide a new alternative for EST-SSR marker validation and a foundation for genetic improvement and conservation strategies for P. amaryllifolius. pine medicine metabolite profiles scarce ESTSSR EST SSR P 157467 157 467 157,46 1084 1 084 1,08 pairs these 66820 66 820 66,82 ESTSSRs SSRs identified 45.5%. 455 45.5% . 45 5 (45.5%) FDM (FDM analysis 7208 7 208 7,20 PCR 8843 8 843 8,84 86.9%, 869 86.9% , 86 9 (86.9%) PIC (PIC 041 0 41 0.41 054 54 0.54 091 91 0.91 India 15746 15 46 157,4 108 08 1,0 6682 6 82 66,8 45.5 4 (45.5% 720 20 7,2 884 84 8,8 86.9 (86.9% 04 0.4 05 0.5 09 0.9 1574 157, 10 1, 668 66, 45. (45.5 72 2 7, 88 8, 86. (86.9 0. (45. (86. (45 (86 (4 (8 (