Holy Hills, sacred groves protected by ethnic minority Dai people, have garnered great interest for conservation in Xishuangbanna—a region containing some of the world's northernmost tropical rain forests and China's richest biodiversity, though much of it has been threatened by deforestation from rubber cultivation. As some of the only remaining forest fragments outside nature reserves, Holy Hills have been documented to contain rare species and ecosystems underrepresented in protected areas. Although previous studies provided some insight into fragmentation impacts, they lacked data to examine population structures. Accordingly, this study uses continuous metrics of tree regeneration for the first time in sacred groves, while also drawing on ethnographic understandings of socioecological contexts of human disturbance, to examine biodiversity and regeneration in three Holy Hills and two nature reserves. Contrary to expectations that smaller area and fragmentation effects would decrease biodiversity in Holy Hills, we found no significant difference in diversity between Holy Hills and nature reserves, though we detected marginally significantly less diversity in seedlings, and certain Holy Hills displayed a shift towards light-demanding species. Common and dominant species varied by site, speaking to the importance of inter-patch beta diversity captured among Holy Hills that can support the maintenance of a regional species pool. Our results also indicated considerable regeneration opportunity in Holy Hills, though individual site conditions and histories had a strong influence. We recommend collaborating with communities and local institutions not only to safeguard existing forest, but also to regenerate and restore fragments whose protection is bolstered with cultural meaning.