Bathymodiolus azoricus is a deep-sea mussel found in the hydrothermal vent fields of the Mid-Atlantic Ridge. It lives in symbiosis with reduced sulfur- and methane-oxidizing γ-proteobacteria within its gills. In our study, we aim to understand the metabolic and physiological interconnections between the symbiotic partners. For this purpose, symbionts and host were pyhsically separated from gill tissue and enriched into separate fractions using density gradient centrifugation. This procedure yielded a symbiont-enriched gradient pellet fraction and a supernatant fraction enriched in host components. The cytosolic and membrane proteome of both these fractions along with whole gill and foot tissue of the mussel were then investigated through 1D-PAGE LC-MS/MS. The spectral counts of the proteins were normalized and relatively quantified using the NSAF method. For efficient identification, sequences from evolutionarily related endosymbiotic and free-living bacteria and from bivalve hosts were compiled in a comprehensive protein database. A total of 3178 proteins were identified from all samples.