javascript:void(0) Hybridization is a potent mechanism for generating genetic diversity and transferring adaptive genetic loci across species or populations (lineages), enabling organisms to explore broader ecological niches. However, the effects of hybridization between species/lineages with different ploidy levels remain underexplored. In this study, we used transcriptomic approaches to investigate the abiotic stress tolerance of common reed (Phragmites australis) and in relation to polyploidy and hybridization. Our findings revealed that a brackish water population of a tetraploid lineage acquired salinity tolerance through adaptive introgression from an octoploid lineage. Among 46 adaptive genes with high FST values between populations, nine were significantly enriched in response to salicylic acid. In a common garden experiment, we chose two hybrid genotypes with similar genetic backgrounds to assess the consistency of adaptability from introgression under varying cadmium (Cd) concentrations. The Heze genotype exhibited a significant decline in net photosynthesis rate and chlorophyll content with increasing Cd concentrations, whereas the Panjin genotype exhibited greater tolerance. Correspondingly, the Heze genotype also had a higher number of differentially expressed genes under both low and high Cd concentrations. These findings suggest that introgressed loci may have varying functions in hybrid populations. This study enhances our understanding of how hybridization between lineages of different ploidy levels can lead to improved stress tolerance and its role in adaptive evolution.