||There is growing interest in linking marine biogeochemistry with marine ecosystems research in response to the increasing need to understand and predict the effect of global change on the marine ecosystem. Such a holistic approach combines oceanographic and biogeochemical processes and information on organisms, ranging from microbes to higher-trophic-levels. Comparative studies offer a means to improve understanding of critical mechanisms that influence marine systems by showing differences in ecosystem response to changing ocean conditions. Comparing similar biomes that differ in a particular set of physical or biological characteristics can provide insight into the susceptibility of the key features of a system to perturbation. Also comparative studies based on long-term observations at fixed time-series stations enable the evaluation of long-term changes in the physical and biological environment, such as those driven by climate patterns. Moreover, the comparative approach provides a feasible alternative to costly and complex research programs designed to provide detailed end-to-end evaluations of marine systems. Planned and unplanned perturbations allow the investigation of the sensitivity of ecosystems and their biogeochemical processes to change at different time and space scales. In well-studied regions where sufficient data are available, models can provide comprehensive syntheses, mechanistic insights and even predictions. We present examples of successful comparative studies that incorporate both biogeochemical and ecosystem aspects. A framework for a basic approach for comparative studies is proposed that considers the interactions between biogeochemical cycles and ecosystems. This approach is based on constructing a minimalistic observational framework grounded within a conceptual model.