One paradox of the trophic biochemistry of the deep sea giant tubeworm Riftia pachyptila, endemic to hydrothermal vent sites and nourished by polyunsaturated fatty acid (PUFA) deficiency chemolitoautotrophic sulfide-oxidizing bacteria, is the source of their PUFAs. Biosynthesis of PUFA starts with two precursors C18:2n-6 and C18:3n-3, which cannot be biosynthesized by most animals due to lack of omega 6- and omega 3-desaturase; thus, C18:2n-6 and C18:3n-3 are generally essential fatty acids for animals. Here, we characterized a gene derived from the R. pachyptila located by hydrothermal vent, which encoded a novel omega 3-desaturase (Rp3Fad). The gene was identified by searching the R. pachyptila transcriptome database using known omega 3-desaturases, and its predicted protein showed 37-45% identical to omega 3-desaturases of fungus and microalgae, and only 31% identitical to nematode Caenorhabditis elegans omega 3-desaturase. Expression in yeast Saccharomyces cerevisiae showed that the Rp3Fad could desaturate C18:2n-6 and C18:3n-6 into C18:3n-3 and C18:4n-3, respectively, displaying a Delta 15 activity similar to plant omega 3-desaturase, but it showed no activity towards C20 n-6 PUFA substrates, differing from the well-characterized C. elegans omega 3-desaturases Delta 5, Delta 6, Delta 8, and Delta 12 activity were also tested, resulting in no corresponding production. The function of omega 3-desaturase identified in R. pachyptila could produce C18:3n - 3 used in synthesis of n - 3 series PUFAs, suggesting an adaption to PUFA deficiency environment in deep sea hydrothermal vent.