Abstract: The rust disease on forest trees is distributed around the world and poses a significant threat to the health of woody plants. As biotrophic parasitic fungi, rust fungi exhibit distinct differences in their infection processes on woody plants compared to other phytopathogenic fungi. It is a hot topic in the field of plant pathology to elucidate the histopathological processes during the infection of rust on woody host plants, as well as the molecular mechanisms underlying the interaction between rust and their hosts at different developmental stages. The widespread application of high-throughput sequencing technology has greatly facilitated the acquisition and in-depth analysis of complex genomic data of rust fungi and their forest host species. Especially, genomic structural analyses of Melampsora larici-populina, Hemileia vastatrix, and Austropuccinia psidii have highlighted the significant role of transposon amplification in host selection and environmental adaptation of rust fungi. Furthermore, the integration of transcriptome based on complete life cycle stages of rust fungi provides valuable insights into the molecular regulation mechanisms of their complex life cycles and biological characteristics. It is one of the key pathways for investigating the molecular interaction mechanisms by characterizing the numerous functions of effector proteins in rust fungi, and significant challenges have arisen in verifying the functions of rust effector proteins dependent on the model plant system. Nonetheless, the molecular interaction mechanisms between rust and host trees with varying resistance levels have achieved good results. Through the association analysis of high-quality genome of rust fungi and forest trees, the improvement of effector protein function verification system and the functional exploration of microbiome in the forest trees-rust fungi interactions, it is expected to promote the research of molecular interaction mechanisms between rust fungi and forest trees into a new stage.