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Black-tailed prairie dogs (Cynomys ludovicianus) are a key component of the disturbance regime in semi-arid grasslands of central North America. Many studies have compared community and ecosystem characteristics on prairie dog colonies to grasslands without prairie dogs, but little is known about landscape-scale patterns of disturbance that prairie dog colony complexes may impose on grasslands over long time periods. We examined spatiotemporal dynamics in two prairie dog colony complexes in southeastern Colorado (Comanche) and northcentral Montana (Phillips County) that have been strongly influenced by plague, and compared them to a complex unaffected by plague in northwestern Nebraska (Oglala). Both plague-affected complexes exhibited substantial spatiotemporal variability in the area occupied during a decade, in contrast to the stability of colonies in the Oglala complex. However, the plague-affected complexes differed in spatial patterns of colony movement. Colonies in the Comanche complex in shortgrass steppe shifted locations over a decade. Only 10% of the area occupied in 1995 was still occupied by prairie dogs in 2006. In 2005 and 2006 respectively, 74 and 83% of the total area of the Comanche complex occurred in locations that were not occupied in 1995, and only 1% of the complex was occupied continuously over a decade. In contrast, prairie dogs in the Phillips County complex in mixed-grass prairie and sagebrush steppe primarily recolonized previously occupied areas after plague-induced colony declines. In Phillips County, 62% of the area occupied in 1993 was also occupied by prairie dogs in 2004, and 12% of the complex was occupied continuously over a decade. Our results indicate that plague accelerates spatiotemporal movement of prairie dog colonies, and have significant implications for landscape-scale effects of prairie dog disturbance on grassland composition and productivity. These findings highlight the need to combine landscape-scale measures of habitat suitability with long-term measures of colony locations to understand the role of plague-affected prairie dogs as a grassland disturbance process.