Although molecular physiology and ecology have drifted apart as a consequence of early separation in the questions posed and techniques used, there is a resurgence of interest in forging links between them. Here we explore the reasons for this renewed interest and provide four examples of how this is happening. Specifically, we examine links between molecular physiology and ecological realities in insect responses to thermal stress, vertebrate responses to anoxia, metabolic fuel use and torpor in mammals, and the recently developed "metabolic theory of ecology." Several novel insights are emerging from integrated approaches to these problems that might not have come forward from any single perspective on them. Nonetheless, prospects for linking molecular physiology and ecological realities are likely to remain poor if greater focus is not given to developing these links. Mostly, this is a consequence of the differing approaches and "languages" adopted by these fields. We discuss approaches by which the prospects for synthetic work might be improved.