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While most of the species in Goodeniaceae family, excluding the <i>Scaevola</i> genus, are endemic to Australasia, <i>S. taccada</i> and <i>S. hainanensis</i> have expanded their distribution range to the tropical coastlines of the Atlantic and Indian Oceans. <i>S. taccada</i> appears to be highly adapted to coastal sandy lands and cliffs, and it has become invasive in places. <i>S. hainanensis</i> is found mainly in salt marshes near mangrove forests, and is at risk of extinction. These two species provide a good system to investigate adaptive evolution outside the common distribution range of this taxonomic group. Here, we report their chromosomal-scale genome assemblies with the objective of probing their genomic mechanisms related to divergent adaptation after leaving Australasia. The scaffolds were assembled into eight chromosome-scale pseudomolecules, which covered 90.12% and 89.46% of the whole genome assembly for <i>S. taccada</i> and <i>S. hainanensis</i>, respectively. Interestingly, unlike many mangroves, neither species has undergone whole-genome duplication. We show that private genes, specifically copy-number expanded genes are essential for stress response, photosynthesis, and carbon fixation. The gene families that are expanded in <i>S. hainanensis</i> and contracted in <i>S. taccada</i> might have facilitated adaptation to high salinity in <i>S. hainanensis</i>. Moreover, the genes under positive selection in <i>S. hainanensis</i> have contributed to its response to stress and its tolerance of flooding and anoxic environments. In contrast, compared with <i>S. hainanensis</i>, the more drastic copy number expansion of <i>FAR1</i> genes in <i>S. taccada</i> might have facilitated its adaptation to the stronger light radiation present in sandy coastal lands. In conclusion, our study of the chromosomal-scale genomes of <i>S. taccada</i> and <i>S. hainanensis</i> provides novel insights into their genomic evolution after leaving Australasia.