With the increasing demand for high-quality tea, the genetic basis of ideal traits of tea plants has been widely concerned. The research on tea tree genomics, specifically focusing on “Longjing 43”, provides significant insights into plant evolution and breeding. “Longjing 43” was chosen due to its complex genome and economic importance. The study successfully assembled its genome to the chromosome level, revealing a large and heterogeneous genome with numerous repetitive sequences. Comparative genomics showed that hybridization has been a key driver of genetic diversity and adaptability in tea plants. These findings are crucial for developing marker-assisted selection (MAS) techniques, improving traits such as disease resistance, flavor, and stress response. Moreover, the research underscores the role of tea tree genomics in preserving cultural heritage and promoting economic benefits through enhanced tea quality. This study contributes to the broader understanding of plant genomics by illustrating the evolutionary processes and potential applications in agriculture, conservation, and industry, thus offering a comprehensive tool for future plant breeding and genetic improvement strategies.