Background  Remnant microhabitats are important for bird habitat selection and plant regeneration in the fragmented habitat. However, empirical information on the consequences of how microhabitat use by birds affects the early recruitment of plants is lacking.

Methods  In this study, we evaluated whether microhabitat selection by the Black Bulbul (Hypsipetes leucocephalus) (J. F. Gmelin, 1789) impacts the early recruitment of the endangered tree species, the Chinese Yew (Taxus chinensis (Pilger) Rehd), in a fragmented forest over a 4-year period (2011–2012, 2018–2019).

Results  Our results showed the main factors affecting H. leucocephalus microhabitat selection were distance to the nearest T. chinensis mature tree, herb cover and density, leaf litter cover, and vegetation type. Moreover, the results of logistic regression also highlighted the importance of elevation, distance to light gap and roads, tree cover in bird microhabitat selection. Furthermore, the seed emergence rate in microhabitats used by birds did not differ from the natural forest, which was related to five factors of bird microhabitat. The Random Forest model showed that seedling emergence rate was increased with leaf litter cover and distance to fallen dead trees, but decreased in relation to herb cover, slope, and elevation.

Conclusion  Our results highlight the importance of remnant microhabitats in fragmented forests for sustaining forest ecology and optimal management. The contribution of microhabitats used by birds to plant recruitment provides insights into how frugivore species contribute to plant regeneration, which should be incorporated in future conservation and management practices of fragmented forests.