Mangrove ecosystems, vital for carbon sequestration and their unique adaptations to inundated environments, face increasing challenges from rising sea levels and elevated atmospheric CO ₂ concentrations due to global climate change. Research is urgently needed to uncover the molecular mechanisms behind mangroves’ responses to these stressors, informing effective conservation and management strategies. In this study, we conducted phenotypic observations and transcriptome analyses on two pioneer mangrove species, Sonneratia apetala and Avicennia marina, under elevated CO ₂ (eCO ₂) and prolonged inundation conditions that simulate future climate scenarios of CO ₂ rise and sea level increase. The two species exhibited distinct morphological and physiological responses: S. apetala showed minimal changes, while A. marina demonstrated accelerated growth and early flowering. Transcriptome analysis revealed molecular-level responses to these stressors, highlighting significant impacts on cell wall biosynthesis, plant hormones, and photosynthesis pathways. This study emphasizes the adaptability of mangroves to climate change and provides insights into their complex responses to eCO ₂ and prolonged flooding. Ultimately, it offers valuable directions for future research on mangrove resilience and climate change adaptation.