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Introducing new variation through genetic rescue has emerged as a promising restoration strategy. However, its success hinges on preserving local adaptation, which has not been studied in the region. To that end, we performed whole\u2010genome sequencing using Illumina next\u2010generation sequencing on 65 gametophyte individuals from our biobank, sourced from 19 sites across Puget Sound. We identified three genetic clusters, corresponding broadly to southern Puget Sound (SPS), Whidbey Basin (WB), and the Strait of Juan de Fuca (SJF). Despite low genetic diversity and high genetic load, we found evidence consistent with local adaptation to five environmental variables. Although salinity emerged as the strongest predictor of environmentally associated genetic variance overall, in SPS the primary drivers were winter sea surface temperature (SST) and seasonal turbidity. We identified environmentally associated variants and enriched gene ontology terms and analysed their allele frequencies to assess functional variation between clusters. These frequencies revealed marked differences between SJF and the other clusters, whereas for most genes the highest\u2010frequency allele in WB was also the most prevalent in SPS. However, for all genes associated with winter SST and turbidity, SPS harboured distinct alleles not found in other clusters. These findings suggest that a WB population may be strong donor candidates for SPS due to higher genetic diversity and shared environmentally associated variation. Further experiments are needed to validate these findings and assess WB suitability for GR.<\/jats:p>","DOI":"10.1111\/mec.70549","type":"journal-article","created":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T12:31:32Z","timestamp":1790166692000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Fine\u2010Scale Genomic Divergence and Local Adaptation in Puget Sound: Implications for Genetic Rescue"],"prefix":"10.1111","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1688-8473","authenticated-orcid":false,"given":"Evelyn","family":"Abbott","sequence":"first","affiliation":[{"name":"Puget Sound Restoration Fund  Bainbridge Island Washington USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3873-4347","authenticated-orcid":false,"given":"Cicero","family":"Alves\u2010Lima","sequence":"additional","affiliation":[{"name":"Centro de Ci\u00eancias do Mar do Algarve Universidade do Algarve  Faro Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jodie","family":"Toft","sequence":"additional","affiliation":[{"name":"Puget Sound Restoration Fund  Bainbridge Island Washington USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0593-3240","authenticated-orcid":false,"given":"Filipe","family":"Alberto","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences University of Wisconsin Milwaukee  Milwaukee Wisconsin USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,23]]},"reference":[{"key":"e_1_2_11_2_1","unstructured":"Alexa A. andJ.Rahnenf\u00fchrer.2026.\u201ctopGO: Enrichment Analysis for Gene Ontology.\u201dR Package Version 2.64.0.https:\/\/bioconductor.org\/packages\/topGO."},{"key":"e_1_2_11_3_1","doi-asserted-by":"publisher","DOI":"10.1101\/2025.07.16.665147"},{"key":"e_1_2_11_4_1","doi-asserted-by":"publisher","DOI":"10.1890\/15\u20101077"},{"key":"e_1_2_11_5_1","doi-asserted-by":"publisher","DOI":"10.3390\/molecules28041585"},{"key":"e_1_2_11_6_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2024.12.025"},{"key":"e_1_2_11_7_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0229703"},{"key":"e_1_2_11_8_1","volume-title":"Nearshore sediment monitoring for the Stormwater Action Monitoring (SAM) Program, Puget Sound, western Washington (Scientific Investigations Report 2018\u20135076)","author":"Black R. 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