Modern pollen morphology provides important information on plant taxonomy, systematics and evolution. Fossil pollen grains have been effectively used in palaeobotany and palaeoecological study. However, it's difficult to identify dispersed fossil pollen grains under traditional light microscope (LM) for those similar pollen types (e.g., species from Poaceae). In recent years, spectroscopic techniques have provided new approaches for detecting pollen chemical composition, thereby improving taxonomic resolution and palaecological implication. Among these techniques, fluorescence lifetime imaging microscopy (FLIM) has attracted increasing attention due to its high resolution, non-destructive, and sensitivity to pollen wall chemistry. In this study, we use FLIM to study Sonneratia pollen, including 6 species (Sonneratia ovata, S. apetala, S. & times; gulngai, S. alba, S. & times; hainanensis, and S. caseolaris). The results demonstrate that FLIM data can effectively classify Sonneratia pollen in four groups: 1) Sonneratia apetala, 2) S. & times; hainanensis, S. caseolaris and S. & times; gulngai, 3) S. ovata, and 4) S. alba. Moreover, the observed classification patterns allow a preliminary assessment of phylogenetic relationships between two hybrid taxa and their parental species. Notably, distinct fluorescence lifetime signatures were identified between the introduced species S. apetala and other native Sonneratia species in China, potentially reflecting differences in their biogeographic histories and ecological adaptations. FLIM provides valuable information on taxonomy, biogeography, and systematics according to our modern pollen examination for Sonneratia. Given FLIM data from fossil pollen can be comparable to extant species, this approach shows potential significance for improving species-level identification of fossil pollen of Sonneratia. Therefore, FLIM opens a new window to understand palaeoecology, evolution history and historical biogeography of tropical mangrove.