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Marine pollen records from the southern South China Sea (SCS) have yielded critical information regarding epicontinental vegetation succession since the last glacial period, which involves understanding the role of tropical rainforests in driving climate change. However, the rich biodiversity and pollen taxa in Southeast Asia are challenging for palynological work, such as detecting pollen signals from various vegetation types and tracing the source areas of pollen grains deposited in the ocean; therefore, improving the taxonomic level of fossil pollen identification is significantly crucial for pollen analysis in tropical regions. To enrich modern pollen references of Southeast Asia, we observed the pollen morphology of 124 identified species (111 genera and 42 families) from tropical Malaysia using a light microscope and scanning electron microscope (SEM). The results show 19 pollen morphotypes, of which the tricolporate type occurs in half of the samples, reflecting the complexity of fossil pollen classification and identification. Pollen sculpture and aperture details of the selected taxa are clearly shown under SEM, which significantly improves the morphological understanding of tropical pollen (e.g., fabaceae , euphorbiaceae , and rubiaceae). This result presents the potential of extracting unique pollen signals to distinguish different vegetation types that contain many common species in Southeast Asia. It highlights the significance of improving pollen identification levels to clarify whether there was a widespread rainforest on the exposed continental shelf during the last glacial period in the southern SCS. • This study showed exine ornamentation and aperture details of the 19 pollen taxa in 124 tropical species. • We improved the identification level for fabaceae , euphorbiaceae , and rubiaceae pollen with high diversity. • This study presented the potential of extracting unique pollen signals to distinguish different vegetation types. [ABSTRACT FROM AUTHOR]