This data was used to investigate the invasion of a non-native disease, plague, to a keystone species, prairie dogs, in Conata Basin, South Dakota, United States. We documented the resulting extent of fragmentation and habitat loss in western grasslands using colony boundaries mapped by the USFS every one to three years from 1993 - 2015. Specifically, we assessed how the arrival of plague in 2008, affected the size, shape, and aggregation of prairie dog colonies, an animal species known to be highly susceptible to plague. As expected the colony complex and the patches in colonies became smaller and more fragmented after the arrival of plague; the total area of each colony and the average area per patch within a colony decreased, the number of patches per colony increased, and average contiguity of each patch decreased, leading to habitat fragmentation.