Meghalaya is well known for its rich tropical biodiversity and numerous natural caves. The Siju Cave of Meghalaya, also known as cave of the bat, is among the longest caves on the Indian subcontinent. The palynological study of fifty bat-guano samples from Siju Cave and of thirty surface soil and moss cushion from the area immediate surrounding the cave reflects the close similarity between the modern pollen and vegetation in the region in the two areas sampled. The resulting palynodata comprise mainly the native flora, dominated by riparian taxa like Duabanga, Syzygium, Careya, and Ficus, along with evergreen and deciduous elements in the region. The evergreen taxa Mesua, Elaeocarpus ,a ndGarcinia, along with Impatiens, reflect the high precipitation in the region. The climate of the region and the vegetation are strongly influenced by the Simsang River, and the heavy rainfall results in the dominance of riparian taxa and other high-rainfall indicator taxa. The occurrence of pollen from Nepenthes khasiana ,a n endemic and endangered plant of Meghalaya, in bat guano is significant and may be due to its insectivorous and entomophilous nature. However, medicinal plants like Swertia chirata, Cinchona, and Rauvolfia are not encountered in the bat-guano sediments, despite their luxuriant growth around the cave, and these species could be avoided by the insects due to their alkaloid contain and bitter taste. The presence of highland taxa such as Pinus, Abies, Picea, and Larix in the bat guano deposit is significant and suggestive of high winds from higher altitudes, or the pollen may be introduced by the return of migratory Siberian birds during winter to the nearby Siju wildlife and bird sanctuary. The recovery of cerealia along with Areca catechu and Citrus pollen indicate the human activity in the region. The abundance of fungal remains, namely Meliola, Glomus, and Microthyriaceae along with degraded palynomorphs are suggestive of strong microbial activity under warm and humid conditions during sedimentation in the region. The main objective of this study is to identify the potential of bat guano for palaeoecological research and as supportive data for surface and sedimentary soil profiles in the South Garo Hills of Meghalaya. The palynodata from the bat guano of the Siju Cave provides a useful source for palaeoecological information for the South Garo Hills, where intensive natural and human-caused forest fires, heavy rainfall, and soil erosion occur every year and there is a relative scarcity of the lake, wetland, and swamp habitats that normally preserve pollen.