Significant climate anomalies have characterized the last 1000 yr in the Sierra Nevada, California, USA. Two warm, dry periods of 150- and 200-yr duration occurred during AD 900–1350, which were followed by anomalously cold climates, known as the Little Ice Age, that lasted from AD 1400 to 1900. Climate in the last century has been significantly warmer. Regional biotic and physical response to these climatic periods occurred. Climate variability presents challenges when interpreting historical variability, including the need to accommodate climate effects when comparing current ecosystems to historical conditions, especially if comparisons are done to evaluate causes (e.g., human impacts) of differences, or to develop models for restoration of current ecosystems. Many historical studies focus on “presettlement” periods, which usually fall within the Little Ice Age. Thus, it should be assumed that ecosystems inferred for these historical periods responded to different climates than those at present, and management implications should be adjusted accordingly. The warmer centuries before the Little Ice Age may be a more appropriate analogue to the present, although no historic period is likely to be better as a model than an understanding of what conditions would be at present without intervention. Understanding the climate context of historical reconstruction studies, and adjusting implications to the present, should strengthen the value of historical variability research to management.