Abstract: Background and Objective: The growth and productivity of banana plants can be disrupted due to water stress. The response of banana plants could be different at the molecular level based on the severity of water stress. This study aimed to profile gene expression in the glycolysis pathway affected by different water stress levels in banana plantlets. Materials and Methods: A transcriptome dataset from four cDNA libraries was used to profile the expression of genes related to cellular respiration. The cDNA libraries were generated from Musa acuminata (genome AAA, cv. Barangan Merah) plantlets treated at different levels of water stress, i.e., low (2.5% PEG), moderate (7.5% PEG) and high (10% PEG). The transcriptome data were analyzed using DAVID, KEGG and DeSeq2 software. Results: Based on DAVID there were 13 genes in glycolysis affected by water stress which were grouped in 6 family proteins. Predominantly, all genes identified in the glycolysis pathway were upregulated in high-stress levels. The 4 family proteins contribute to pyruvate metabolism, while 2 family proteins contribute to fermentative metabolism. It could be indicated that water stress led to hypoxia, so the energy must be produced using anaerobic metabolism. The MaFBA6, MaFBA8 and MaPDCB genes were selected and used to validate mRNa-seq and transcriptome analysis. Conclusion: Banana plantlets respond to water stress by increasing the expression of glycolysis-related genes. With transcriptomic analysis, respiration-related genes can be identified to add to regarding banana plants’ response to water stress.