Sargassum fusiforme and Sargassum thunbergii are ecologically and commercially important seaweeds that thrive in intertidal zones and are frequently exposed to extreme variation in environmental stress. Despite their importance, limited genomic information exists for these species, which hinders a comprehensive understanding of the evolution and adaptation of the genus Sargassum to marine coastal habitats. Two Sargassum genomes were generated in this study. The genome sizes of S. fusiforme and S. thunbergii were 438 and 376 Mbp, respectively, which are larger than the published genomes of the brown seaweed group, Ectocarpales. Expansion of the Sargassum genomes was significantly explained by the spread of transposable elements (TEs). Additionally, extensive gene duplications and their diversification occurred particularly through tandem, proximal, and dispersed duplications, which likely played an important role in response to environmental stress. Differentially expressed gene analysis under ambient and desiccation stress conditions confirmed that some duplicated genes respond to stress. We identified enhanced disease susceptibility 1 (EDS1) genes that promote salicylic acid (SA) biosynthesis, and their expansion is likely linked to TEs. We also confirmed the potential role of EDS1 by analyzing its subcellular localization (in Arabidopsis thaliana) and quantified the increased SA levels under desiccation conditions. This study demonstrates that the genomic evolution has played a critical role in allowing S. fusiforme and S. thunbergii to adapt to harsh intertidal conditions. The genomic resources of Sargassum species provided here will be instrumental in advancing future research, aiding in the understanding of adaptive evolution in brown algae.