Little is known about the life of marine microorganisms under their particular environmental conditions. Genome sequencing combined with the techniques of functional genomics, especially proteome analyses, now open up revolutionary insights into the adaptation strategies marine organisms have evolved in response to the challenges of their habitat. This report summarizes the first approaches and state-of-the-art in the field of proteome analysis of marine bacteria. This includes, amongst others, proteomics on culturable, free-living marine bacteria and on uncultivable bacteria living in symbiosis with higher organisms. Finally, new approaches to determine the metaproteome of uncultured microbial consortia from marine habitats are discussed.