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We discuss the ecology of Anaplasma phagocytophilum and Borrelia burgdorferi in the western U.S. These agents, while emerging in the eastern U.S., remain stable or rare in the west. In the western U.S., tick vectors and mammalian hosts for B. burgdorferi and A. phagocytophilum are distinct from those in the eastern U.S. and considerably more variable. Spatial complexity, local extinctions, and low levels of movement among foci may determine the distribution and prevalence of these agents. High-prevalence A. phagocytophilum patches may be transient, possibly as host individuals become immune. Thus, A. phagocytophilum in California could exist in a metapopulation of interacting patches. Local dynamics are sensitive to host population sizes and minimum tick infestation levels. Determining critical values for these key factors and their interactions will be important for predicting the level and distribution of future infections in the western U.S.