The important role of humans in the development of current ecosystems was recognized decades ago; however, the integration of history and ecology in order to inform conservation has been difficult. We identified four issues that hinder historical ecological research and considered possible solutions. First, differences in concepts and methods between the fields of ecology and history are thought to be large. However, most differences stem from miscommunication between ecologists and historians and are less substantial than is usually assumed. Cooperation can be achieved by focusing on the features ecology and history have in common and through understanding and acceptance of differing points of view. Second, historical ecological research is often hampered by differences in spatial and temporal scales between ecology and history. We argue that historical ecological research can only be conducted at extents for which sources in both disciplines have comparable resolutions. Researchers must begin by clearly defining the relevant scales for the given purpose. Third, periods for which quantitative historical sources are not easily accessible (before AD 1800) have been neglected in historical ecological research. Because data from periods before 1800 are as relevant to the current state of ecosystems as more recent data, we suggest that historical ecologists actively seek out data from before 1800 and apply analytic methods commonly used in ecology to these data. Fourth, humans are not usually considered an intrinsic ecological factor in current ecological research. In our view, human societies should be acknowledged as integral parts of ecosystems and societal processes should be recognized as driving forces of ecosystem change. © 2011 Society for Conservation Biology.