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Highly differentiated genomic regions, known as genomic islands, often evolve between diverging lineages. These genomic islands may be related to selection promoting adaptation or reproductive isolation. Based on whole genome assembly and genome\u2010wide RAD sequencing in a pair of yellow croakers (genus: <jats:italic>Larimichthys<\/jats:italic>), we investigated the evolutionary processes shaping genomic landscapes of divergence. Demographic modelling indicated that the two species diverged following a secondary contact scenario, where differential introgression and linked selection were suggested to be involved in heterogeneous genomic divergence. We identified reduced recombination rate in genomic islands and a relatively good conservation of both genetic diversity and recombination landscapes between species, which highlight the roles of linked selection and recombination rate variation in promoting heterogeneous divergence in the common ancestral lineage of the two species. In addition, we found a positive correlation between differentiation (<jats:italic>F<\/jats:italic><jats:sub>ST<\/jats:sub>) and absolute sequence divergence (<jats:italic>D<\/jats:italic><jats:sub>xy<\/jats:sub>), and elevated <jats:italic>D<\/jats:italic><jats:sub>xy<\/jats:sub> in genomic islands, indicating that the genomic landscape of divergence was not shaped by linked selection alone. Restricted gene flow in highly differentiated regions has probably remodelled the landscape of heterogeneous genomic divergence. This study highlights that highly differentiated genomic regions can also arise from a combination of linked selection and differential gene flow in interaction with varying recombination rates.<\/jats:p>","DOI":"10.1111\/mec.16693","type":"journal-article","created":{"date-parts":[[2022,9,16]],"date-time":"2022-09-16T06:34:41Z","timestamp":1663310081000},"page":"5729-5744","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":25,"title":["Linked selection, differential introgression and recombination rate variation promote heterogeneous divergence in a pair of yellow croakers"],"prefix":"10.1111","volume":"31","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3363-5753","authenticated-orcid":false,"given":"Le","family":"Wang","sequence":"first","affiliation":[{"name":"State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences Sun Yat\u2010sen University  Guangzhou China"},{"name":"Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore  Singapore City Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3766-2932","authenticated-orcid":false,"given":"Shufang","family":"Liu","sequence":"additional","affiliation":[{"name":"Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences &amp; 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