Conservation genomics provides insights into genetic resilience and adaptation of the endangered Chinese hazelnut, .

Global climate change has increased concerns regarding biodiversity loss. However, many key conservation issues still required further research, including demographic history, deleterious mutation load, adaptive evolution, and putative introgression. Here we generated the first chromosome-level genome of the endangered Chinese hazelnut, , and compared the genomic signatures with its sympatric widespread - complex. We found large genome rearrangements across all species and identified species-specific expanded gene families that may be involved in adaptation. Population genomics revealed that both . and the - complex had diverged into two genetic lineages, forming a consistent pattern of southwestern-northern differentiation. Population size of the narrow southwestern lineages of both species have decreased continuously since the late Miocene, whereas the widespread northern lineages have remained stable (. ) or have even recovered from population bottlenecks (- complex) during the Quaternary. Compared with - complex, . showed significantly lower genomic diversity and higher inbreeding level. However, . carried significantly fewer deleterious mutations than - complex, as more effective purging selection reduced the accumulation of homozygous variants. We also detected signals of positive selection and adaptive introgression in different lineages, which facilitated the accumulation of favorable variants and formation of local adaptation. Hence, both types of selection and exogenous introgression could have mitigated inbreeding and facilitated survival and persistence of . . Overall, our study provides critical insights into lineage differentiation, local adaptation, and the potential for future recovery of endangered trees.