Background/Objectives: Chemosymbiotic bivalves play a fundamental role in deep-sea cold seep and hydrothermal vent ecosystems, where essential long-chain polyunsaturated fatty acids (LC-PUFAs) are scarce. Whether these bivalves retain the capacity for endogenous PUFA synthesis remains poorly understood. Here, we investigated the PUFA biosynthetic capacity of two dominant chemosymbiotic bivalves from the Haima cold seep—the mussel Gigantidas haimaensis and the clam Archivesica marissinica. Methods: Genome and transcriptome assembly revealed three fatty acid desaturase (Fad) genes per species, which phylogenetically clustered into Δ5 (GhFads1, GhFads2; AmFads1, AmFads2) and Δ6/8 (GhFads3, AmFads3) clades, with lineage-specific duplications within the Δ5 clade. Functional assays were performed in yeast to characterize the activity of these enzymes. Results:Both Fads3 enzymes (Δ6/8 clade) convert C20:3n-6 and C20:4n-3 into C20:4n-6 and C20:5n-3, respectively, exhibiting Δ8-desaturase activity. Notably, Δ5-clade isoforms showed divergent substrate specificities: GhFads2 and AmFads1 functioned as classical Δ5-desaturases on PUFA substrates, whereas GhFads1 and AmFads2 specifically desaturated the bacterial monounsaturated fatty acid (MUFA) C18:1n-7 to produce C18:2n PUFAs. Conclusions: Together, our results reveal that cold-seep bivalves retain endogenous LC-PUFA biosynthetic capacity and have evolved duplicated Δ5-desaturases with novel regioselectivity toward bacterial MUFAs, likely representing an adaptive membrane modification for survival under extreme deep-sea conditions.