Oyster and seawater sampling: Juvenile oysters (Pathogen free animals produced in hatchery) and seawater were sampled in Thau Lagoon (Languedoc-Roussillon, France) in October 2015 during a mortality event. Seawater wassize-fractionated by sequential filtration as described by Bruto et al., 2016.Bacterial sampling: Oysters and large seawater particles fractions (> 60μm) were ground (Ultra-Turrax, IKA) and 100μL were plated on Vibrio selective media (thiosulfate-citrate-bile salts sucrose agar, TCBS). The others filters (5, 1 and 0.22 μm) were directly placed on TCBS agar plate and incubated 2 days at 20°C. Around 100 colonies for each sample were randomly picked, re-steaked first on TCBS and then on Zobell agar (4g.L-1bactopeptone, 1 g.L-1yeast extract and 15g.L-1agar in sterile

seawater, pH 7.4) and stock cultures were stored at −80 °C in Zobell containing 15% glycerol (v/v). Population structure analysis: Isolates were first genotyped trough an hsp60 genepartial sequence as described previously (Goh, Potter, Wood, & Hemmingsen, 1996; Hunt et al., 2008) generating a total of 437 hsp60 sequences. MLST genotyping : Secondly, to validate the taxonomic affiliation of the isolates assigned to Harveyi clade, 3 additional protein-coding genes were sequenced (rctB, topA and mreB).