Bacterial symbiosis and/or parasitism is widespread in hydrothermal bivalves, and is typically developed in gills, with a lower incidence in mantle and digestive glands, while it has never been described in byssus. Using ultrastructural examination, we provide evidence for the existence of a potentially new group of filamentous prokaryotic organism in Bathymodiolus azoricus byssus, with putative parasitic influence. Additionally, a cystic, undefined organism was found with an unclear physiological role within the spongy net of the byssus plaque. Our results indicate that in spite of its antibacterial protective sheath, byssus gives access to prokaryotic organisms becoming prone to failure through damaged collagen fibres.