Although introduced hemosporidian (malaria) parasites (Apicomplexa: Haemosporida) have hastened the extinction of endemic bird species in the Hawaiian Islands and perhaps elsewhere, little is known about the temporal dynamics of endemic malaria parasite populations. Haemosporidian parasites do not leave informative fossils, and records of population change are lacking beyond a few decades. Here, we take advantage of the isolation of West Indian land-bridge islands by rising postglacial sea levels to estimate rates of change in hemosporidian parasite assemblages over a millennial time frame. Several pairs of West Indian islands have been connected and separated by falling and rising sea levels associated with the advance and retreat of Pleistocene continental glaciers. We use island isolation following postglacial sea-level rise, ca. 2.5 ka, to characterize long-term change in insular assemblages of hemosporidian parasites. We find that assemblages on formerly connected islands are as differentiated as assemblages on islands that have never been connected, and both are more differentiated than local assemblages sampled up to two decades apart. Differentiation of parasite assemblages between formerly connected islands reflects variation in the prevalence of shared hemosporidian lineages, whereas differentiation between islands isolated by millions of years reflects replacement of hemosporidian lineages infecting similar assemblages of avian host species.avian malaria | bananaquit | beta diversity | Plasmodium | Haemoproteus I nsular biotas provide natural laboratories for characterizing change in host-parasite relationships over time (1). Haemosporidian parasites (genera Plasmodium and Haemoproteus, among others) are dipteran vector-transmitted protozoans that reproduce clonally in cells of vertebrates and cause symptoms referred to as malaria (2). The few fossils of ancient hemosporidians (3) are insufficient to analyze retrospectively the dynamics of these hostparasite interactions. We have found that hemosporidian parasite assemblages of birds present remarkable geographic heterogeneity in the West Indies, even though common avian host species are widely distributed throughout the archipelago (4). Additionally, the frequencies of individual lineages in assemblages of avian hemosporidian parasites have been observed to vary over periods as short as one decade (5-7). Here, we take advantage of the geographic history of islands in the West Indies to characterize changes in avian hemosporidian parasite assemblages over millennial time scales.During the late Quaternary glaciations, which reached their maximum extent ca. 26 ka, an increase in continental ice volume caused the global sea level to drop by as much as 120 m, exposing land connections between islands lying on shallow banks (8). During periods of sea level lows, organisms could freely disperse between some pairs of present-day islands, tending to homogenize assemblages of birds and, presumably, their pathogens (8). Deglaciation started 7.5-10 ka, and ended...