Abstract Durian (Durio zibethinus Murr.) fruits are famous for their unique aroma. This study analysed the Durian fruit transcriptome to discover the expression patterns of genes and to understand their regulation. Three developmental stages of Durian fruit, namely, early [90 days post-anthesis (DPA)], mature (120 DPA), and ripen (127 DPA), were studied. The Illumina HiSeq platform was used for sequencing. The sequence data were analysed using four different mapping aligners and statistical methods: CLC Genomic Workbench, HISAT2+DESeq2, Tophat+Cufflinks, and HISAT2+edgeR. The analyses showed that over 110 million clean reads were mapped to the Durian genome, yielding 19,976, 11,394, 17,833, and 24,351 differentially expressed genes during 90-127 days post-anthesis. Many identified differentially expressed genes were linked to the fruit ripening processes. The data analysis suggests that most genes with increased expression at the ripening stage were primarily involved in the metabolism of cofactors and vitamins, nucleotide metabolism, and carbohydrate metabolism. Significantly expressed genes from the young to mature stage were mainly associated with carbohydrate metabolism, amino acid metabolism, and cofactor and vitamin metabolism. The transcriptome data will serve as a foundation for understanding Durian fruit development-specific genes and could be helpful in fruit’s trait improvement. Durio Murr. Murr aroma regulation namely 90 [9 postanthesis post anthesis DPA, DPA , (DPA)] 120 (12 DPA) 127 studied sequencing methods Workbench HISAT2DESeq2 HISATDESeq HISAT2 DESeq2 HISAT DESeq HISAT2+DESeq2 TophatCufflinks Tophat Cufflinks Tophat+Cufflinks HISAT2edgeR HISATedgeR edgeR HISAT2+edgeR 11 genome 19976 19 976 19,976 11394 394 11,394 17833 17 833 17,833 24351 24 351 24,35 90127 90-12 postanthesis. anthesis. processes vitamins developmentspecific development specific s improvement 9 [ (DPA) 12 (1 HISAT2DESeq HISAT2+DESeq 1 1997 97 19,97 1139 39 11,39 1783 83 17,83 2435 2 35 24,3 9012 90-1 (DPA ( 199 19,9 113 3 11,3 178 8 17,8 243 24, 901 90- 19, 11, 17,