AbstractThis study aimed to characterise D24, D99, D160, D168, D197 and D200 varieties at matured, riped, and dehisced stages through morphological observation and molecular characterisation using transcriptomic analysis. Twenty-eight morphological traits were evaluated according to durian descriptor _National Guidelines for The Conduct of Tests for Distinctness, Uniformity and Stability_. Separately, a total of 21 durian samples were submitted to transcriptome analysis to access biosynthesis pathways during fruit developmental stages. The results of the study showed that these six Malaysian durian varieties demonstrated a considerable level of morphological variation. Statistical ANOVA and canonical discriminant analysis identified pedicel length trait as the most significant quantitative trait to differentiate the six varieties. Qualitative traits dendrogram clustered the varieties into two main clades includes Clade A (mostly of D160, D168, D197 and D200) and Clade B (mostly of D24 and D99).....