The physical climate system is dominated by a range of space and time scales associated with modes of natural variability. The TOGA program enhanced our understanding and predictive capability for the El Nino Southern Oscillation (ENSO) phenomenon, especially as it pertained to the tropical Pacific Ocean and connections to the global atmosphere. Similarly, the WOCE program established a solid foundation to study the ocean’s role in climate on a global scale. The present WCRP CLIVAR program picks up where TOGA and WOCE left off and has as its goal to describe and understand the physical processes responsible for climate variability and predictability on seasonal, interannual, decadal, and centennial time-scales. Modes of natural variability such as ENSO, the North Atlantic Oscillation, the Pacific Decadal Oscillation, and monsoonal circulations are central to the research agenda for the physical climate system. Because of the dominant attributes of these modes in the coupled ocean-atmosphere system, their influence projects onto key aspects and controls of marine ecosystems such as temperature, nutrients, upwelling, and mixed layer properties. The effects of the coupled ocean-atmosphere climate system impact marine ecosystems from primary production all the way to the highest trophic levels of the marine food chain. As such, these modes of natural variability provide a useful construct for studying interactions between climate variability and marine ecosystems. However, such interdisciplinary research need not, and should not, be viewed solely in a forced or one-way scenario of atmosphere-ocean coupling impacting marine ecosystems. Rather the potential exists for true interactive coupling between marine ecosystems and the physical climate system ranging from the influence of phytoplankton distributions on the depth of penetrating radiation and the upper ocean heat budget to the emission of dimethyl sulfide and associated cloud condensation nuclei.