Despite high biodiversity and endemism and decades of research, the tree diversity of the Eastern Himalaya remains poorly understood. To fulfill this gap, we examined the patterns of the alpha and beta diversity and tree community structure in the Darjeeling area of the Eastern Himalaya. We conducted primary vegetation sampling focused on the tree strata within 3 protected areas, including National Park (NP) and Wildlife Sanctuary (WLS) of the Darjeeling Himalaya, India. The study sites included Mahananda WLS, Neora Valley NP, and the lower and upper ranges of Singalila NP. A total of 32 sampling plots (each 200 m x 200 m) were established across these sites, within which 128 quadrats (20 m × 20 m) were laid out for detailed vegetation analysis. Within each quadrat, all trees with a girth at breast height (GBH) of ≥ 10 cm were measured and identified. We recorded a total of 2137 individuals belonging to 65 tree species, 47 genera and 31 families in our study. Out of all the recorded tree species, 5 species were found endemic to the Eastern Himalayan region, and 4 globally threatened as per the IUCN Red List. We observed the highest alpha and beta diversity in the temperate forests of lower Singalila NP. Tree basal area and the density were highest in the tropical moist deciduous forests of Mahananda WLS and the sub-alpine forests of upper Singalila NP, respectively. The study sites showed distinct tree community assemblages with high beta diversity determined by substitution components. We identified 27 indicator tree species (including 23 species from single sites) with significantly high Indicator Value (IndVal) across the different forest types of the Darjeeling Himalaya. We conclude that different forest types in the Darjeeling Himalaya support a high diversity and a unique assemblage of trees, including endemics. For efficient conservation of plant diversity in the Himalaya, there is an urgent need to create more protected areas.