Bathymodiolus thermophilus is a mixotrophic mussel capable of deriving nourishment from sulphur-oxidizing, bacterial endosymbionts in its gills and from suspended particulates through mucociliary feeding. These mussels become nutritionally stressed when removed from sulphide-rich fluid, but the dynamics of the host/symbiont relationship during this process are still not fully understood. Bathymodiolus thermophilus mussels were collected from an active and a waning hydrothermal site on the southern East Pacific Rise (EPR) and were removed from active venting for 12 d at a site on the northern EPR. Light and transmission electron microscopy showed that gill symbionts were lost from gill bacteriocytes in transplant mussels and that mussels exposed to longer periods of sulphide deprivation suffered deterioration of gill structure and body condition. There was no evidence to support the hypothesis of a shift toward reliance on photosynthetically derived organic material in mussels at the waning vent site.