Recognizing the many links between biogeochemical reactions and the uncharacterized microorganisms populating the oceans, microbiologists have undertaken a major effort in the past decade to explore the marine microbial biosphere. Meanwhile, many earth scientists now view ocean chemistry as highly dynamic on geologic time scales, reflecting changing inputs and outputs as Earth and life co-evolved. Research at an emerging network of ancient ocean analog sites is poised to improve our knowledge of changes in past ocean states, partly by revealing how we should interpret hopanoid and carotenoid biomarkers for marine phototrophs. Our long-term goal is a mechanistic understanding of interactions between physical and chemical factors and the ecology of anoxygenic and oxygenic phototrophy, including biosignatures.