Majority of global biodiversity databases lack sufficient coverage from the developing world and thus severely limiting their worldwide applicability. Bridging these knowledge gaps in global databases merits urgent research priority in biodiversity science. Here, we present Trees of India (ToI), Version-I, a comprehensive database assembled from an extensive literature synthesis of 313 studies published from 1872 to 2022. Based on the ToI database, we aimed to investigate the patterns of diversity, distribution, endemic and threat status of the tree flora of India. We recorded 3708 tree species across India, which raises the number by more than one-third (1199 species) previously reported for this mega-biodiverse country in GlobalTreeSearch (GTS). We found 93 species erroneously included for India as tree lifeform in the GTS. The distribution of the tree flora considerably varied across the states in India, with southern and eastern parts harbouring the highest tree diversity. We found evidence of distance decay in compositional similarity among the states in India. Our results reveal that 609 tree species are endemic to the country and 347 species are currently threatened. We also found a linear positive correlation between the endemic and threatened tree species pool of the country. Our data synthesis on the trees of India has huge policy and management implications in guiding biodiversity conservation, ecosystem restoration and climate change mitigation in this most populous country of the world. Looking ahead, our study showcases a model with learnings for other countries/regions/taxa to bridge the existing knowledge gaps in global biodiversity databases.