Aims <p>Endophytic nitrogen (N) fixation represents a crucial N acquisition strategy for non-nodulating plants in N-limited ecosystems. However, fundamental aspects of endophytic diazotrophs, including their community structure, potential source, and inter-niche migration patterns, remain poorly characterised.</p> Methods <p>In this study, we investigated the community composition and diversity of endophytic diazotrophs within different tissues (leaf, twigs, and root) of <i>Platycladus orientalis</i> inhabiting rocky mountainous regions using Illumina Miseq sequencing of the <i>nifH</i> gene. Additionally, we analysed their seasonal variations (wet and dry season) and tissue-specific distribution patterns. Source tracking analysis was used to quantitatively evaluate the potential source and transmission pathways of these N₂-fixing bacteria.</p> Results <p>Endophytic diazotrophs were dominated by the class Alphaproteobacteria (49.4%–84.3%), with <i>Bradyrhizobium</i> and <i>Skermanella</i> being the predominant genera. The community composition of diazotrophs was significantly affected by the season (<i>P</i> = 0.001) and tissue type (<i>P</i> = 0.001). However, no statistically significant differences were observed in diazotroph diversity across seasons or tissue types (<i>P</i> &gt; 0.05). Source tracking analysis revealed that the rhizosphere soil contributed 57.45% and 25.03% of the endophytic diazotrophs within the root and twig, respectively, whereas the leaf phyllosphere contributed relatively less (0.01%–18.12%). Furthermore, only a small proportion (7.09%–19.78%) of N₂-fixing bacteria migrated between the phyllosphere, leaf, and twigs.</p> Conclusions <p>These results highlight the differences in endophytic diazotroph community structure across seasons and tissue types, revealing their sources and migration patterns. Our findings may guide the development and utilisation of these microbial resources for N₂ fixation.</p>