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Introduction Tidal inundation, characterized by its duration and depth, is a fundamental driver of mangrove zonation and community assembly. A mechanistic understanding of how mangrove species, particularly those with restricted ranges, adapt to this dual hydrological stress is critical for informing conservation and restoration strategies under changing environmental conditions. This study examined the combined effects of flooding duration and depth on seedlings of two thermophilic mangrove species with narrow distributions in China: Lumnitzera littorea and Scyphiphora hydrophyllacea . Methods A controlled tidal simulation system was employed to apply nine interactive treatments, combining three flooding durations (4, 8, and 12 h·d −1 ) with three depths (0, 20, and 40 cm). A comprehensive suite of seventeen functional traits was measured, encompassing seedling growth, biomass allocation, root morphology, and root anatomical structure. Results For L. littorea , growth, biomass accumulation, and root morphological were optimal under a specific, narrow range of flooding conditions (4 h·d −1 & 20 cm), highlighting a limited flooding tolerance. In contrast, S. hydrophyllacea exhibited maximal performance across most measured traits, including adaptive modifications in root anatomy (cortical thickness, stele proportion), particularly under the 8 h·d −1 & 20 cm treatment, indicating greater phenotypic plasticity. Principal component analysis further underscored these distinct adaptive strategies: L. littorea relied on a tightly correlated suite of traits centered on basal diameter, biomass, and root morphology, while S. hydrophyllacea utilized a multidimensional strategy coordinating height, diameter, biomass, and root anatomy traits. Conclusion Our findings reveal that co-occurring mangrove species adopt divergent ecological strategies to cope with identical dual flooding stress; these strategies span a continuum from conservative specialization to plastic generalization. This study provides a trait-based framework for understanding niche differentiation and advances species-specific selection criteria for restoring vulnerable mangroves in heterogeneous intertidal environments.