The Zingiberaceae family represents one of the most diverse monocot lineages in tropical Asia; however, the species delimitation of Amomum s.l. remains challenging due to morphological convergence and limited molecular evidence. This study analyzed transcriptomic data from seven Amomum s.l. species in Peninsular Malaysia to evaluate their evolutionary relationships and examine variation across chloroplast genes. RNA sequencing and de novo assembly identified 85 chloroplast protein-coding genes, of which 43 complete genes were retained for subsequent analyses. Comparative assessment revealed conserved genome features, including GC content ranging between 37.4% and 38.0%, alongside lineage-specific divergence in codon usage bias and expression profiles. Heatmap clustering of normalized gene expression patterns indicated distinct transcriptional signatures, particularly in A. elan, suggesting species-specific regulatory divergence. Nucleotide diversity (π) analysis identified hotspots in ndhJ, psbT, psbZ, and rps14, highlighting their potential as molecular markers for improving species delimitation, whereas core genes such as rbcL and psbA remained highly conserved, reducing their effectiveness in distinguishing species-level variation. Phylogenetic reconstruction using Bayesian inference (BI) and maximum likelihood (ML) approaches, based on 43 concatenated chloroplast genes (28,794 bp), supported the paraphyly of Amomum s.l., with Peninsular Malaysian species distributed across multiple clades. Amomum trilobum showed a closer association with Wurfbainia than with Amomum–Alpinia, suggesting the possible transfer of the species to Wurfbainia with further taxonomic evaluation. These findings highlight the important roles of genomic and morphological datasets in understanding the evolutionary relationships in Amomum s.l. and offer new molecular insights into the evolution of Zingiberaceae in Peninsular Malaysia.