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While it harbors diverse virulence factors, its disease mechanisms remain poorly understood. To address this, we sequenced 82 environmental isolates from the Baltic Sea and combined them with 325 published genomes (clinical and environmental) for comparative analysis. Phylogenetic reconstruction revealed four major lineages, with Baltic strains restricted to L2 and L4. Clinical and environmental strains were found across all lineages, suggesting phylogeny reflects environmental adaptation more than pathogenicity. Using our newly developed PhyloBOTL pipeline, we identified 128 orthologs enriched in clinical isolates, grouped into 36 co-localization clusters. These include both known and novel virulence candidates, such as chaperone-usher pili, type VI secretion effectors, and spermidine synthases. Some clusters showed convergent loss across clades, implying niche-specific evolution. We also designed PCR primers targeting these genes to aid in the surveillance of pathogenic\n                      <jats:italic toggle=\"yes\">V. vulnificus<\/jats:italic>\n                      strains.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        <jats:italic toggle=\"yes\">Vibrio vulnificus<\/jats:italic>\n                        is a naturally occurring marine bacterium that can cause life-threatening infections, with incidence increasing as coastal waters warm due to climate change. Determining which environmental strains pose the greatest risk remains a major challenge for public health surveillance. By analyzing hundreds of genomes from globally distributed strains, including extensive sampling from the rapidly warming Baltic Sea, this study shows that pathogenic potential is not restricted to specific evolutionary lineages but is instead associated with distinct sets of genes enriched in clinical strains. To support pathogen detection, we developed PCR primers targeting a subset of these clinically associated genes. Together, these findings provide new insight into the molecular basis of\n                        <jats:italic toggle=\"yes\">V. vulnificus<\/jats:italic>\n                        infections and offer practical tools for improved detection, monitoring, and risk assessment of harmful strains in coastal waters and seafood under ongoing climate change.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/mbio.00205-26","type":"journal-article","created":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T13:01:02Z","timestamp":1781701262000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Phylogeny-aware comparative genomics of\n                    <i>Vibrio vulnificus<\/i>\n                    links genetic traits to pathogenicity"],"prefix":"10.1128","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7850-5285","authenticated-orcid":true,"given":"Luis F.","family":"Delgado","sequence":"first","affiliation":[{"name":"KTH Royal Institute of Technology, SciLifeLab","place":["Stockholm, Sweden"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-0221-6772","authenticated-orcid":false,"given":"David J.","family":"Riedinger","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03xh9nq73","id-type":"ROR","asserted-by":"publisher"}],"name":"Leibniz Institute for Baltic Sea Research Warnem\u00fcnde (IOW)","place":["Rostock, Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8090-5154","authenticated-orcid":true,"given":"V\u00edctor","family":"Fern\u00e1ndez-Ju\u00e1rez","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/035b05819","id-type":"ROR","asserted-by":"publisher"}],"name":"University of Copenhagen","place":["Helsing\u00f8r, Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8100-4649","authenticated-orcid":false,"given":"Daniel P. 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