In this study we performed a phenotypic and genotypic screening for the identification of omega-3 fatty acid producers in bacterial strains isolated from 5, 500, and 1000 m deep coastal seawater from the Bay of Biscay. We further measured EPA production in pelagic Vibrio sp. strains collected at the three different depths, and sequenced the genomes of two representative strains of EPA producing and non-producing Vibrio strains.