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To investigate the genomic changes underlying the evolution of sexual determination, we sequenced a chromosome\u2010level genome, multitissue transcriptomes, and reduced representation population data for the Atlantic halibut (<jats:italic>Hippoglossus hippoglossus<\/jats:italic>), which has an XY\/XX sex determination mechanism and has recently diverged (0.9\u20133.8\u00a0Ma) from the Pacific halibut (<jats:italic>Hippoglossus stenolepis<\/jats:italic>), which has a ZZ\/ZW system. We used frequency and coverage\u2010based population approaches to identify a putative sex\u2010determining factor, <jats:italic>GSDF<\/jats:italic>. We characterized regions with elevated heterozygosity and linkage disequilibrium indicating suppression of recombination across a nascent sex chromosome. We detected testis\u2010specific expression of <jats:italic>GSDF<\/jats:italic>, the sequence of which is highly conserved across flatfishes. Based on evidence from genome\u2010wide association, coverage, linkage disequilibrium, testis and brain transcriptomes, and sequence conservation with other flatfishes, we propose a mechanism for the recent evolution of an XY sex\u2010determination mechanism in Atlantic halibut. Changes to the ancestral sex\u2010determining gene <jats:italic>DMRT1<\/jats:italic> in regulating the downstream gene <jats:italic>GSDF<\/jats:italic> probably coincided with <jats:italic>GSDF<\/jats:italic>, or a proximal regulatory element of it, becoming the primary sex\u2010determining factor. Our results suggest changes to a small number of elements can have drastic repercussions for the genomic substrate available to sex\u2010specific evolutionary forces, providing insight into how certain elements repeatedly evolve to control sex across taxa. Our chromosome\u2010level assembly, multitissue transcriptomes, and population genomic data provide a valuable resource and understanding of the evolution of sexual systems in fishes.<\/jats:p>","DOI":"10.1111\/1755-0998.13369","type":"journal-article","created":{"date-parts":[[2021,3,3]],"date-time":"2021-03-03T07:51:02Z","timestamp":1614757862000},"page":"1686-1696","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":32,"title":["Chromosome level reference of Atlantic halibut <i>Hippoglossus<\/i><i>hippoglossus<\/i> provides insight into the evolution of sexual determination systems"],"prefix":"10.1111","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4588-3479","authenticated-orcid":false,"given":"Anthony L.","family":"Einfeldt","sequence":"first","affiliation":[{"name":"Biology Department Dalhousie University Halifax NS 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