All five species of prairie dogs were once common across the central and western grasslands  of North America, likely more than one billion strong. But the widespread destruction of prairie dog colonies and the arrival of exotic diseases in the 1900s reduced prairie dogs by more than 95 percent. Today they exist in relatively small colonies scattered across 12 states in the U.S., one Mexican state, and one Canadian province.
Because of their precipitous decline since the 1800s, the U.S. Fish and Wildlife Service (FWS) placed black-tailed prairie dogs on the “candidate list” of threatened species in 1998. Before a final decision was made, some states and federal agencies began taking conservation measures by regulating the shooting and poisoning of prairie dogs on some federal lands. Prairie dog colonies began to expand once more, and in August 2004, FWS bowed to political pressure and removed prairie dogs from the candidate list. The very next day, the U.S. Forest Service announced plans to begin mass poisoning of prairie dogs on national grasslands in South Dakota and Nebraska. Since then, other states have also dramatically curtailed their conservation programs, once again jeopardizing prairie dog recovery.
Humans pose the greatest threat to prairie dogs, frequently poisoning and shooting the animals when they consider them pests. Many ranchers dislike the animals because they eat grass that ranchers would rather have for their livestock.
Sylvatic plague—an exotic disease that entered North America in 1900—is also threatening prairie dogs’ survival. Prairie dogs have no known immunity to plague, which has now impacted almost all areas where prairie dogs occur. Plague often eliminates most or all prairie dogs in an area within days. In 2008 it struck Conata Basin, South Dakota – the largest and most important complex of prairie dog colonies remaining on public land in the Great Plains. About 20,000 acres of the 30,000 acres of prairie dog colonies were lost.
Prairie dog colonies occur only within central and western grasslands and shrublands. Much of the original grassland habitat in North America has been plowed for agriculture, and very little of these grasslands are protected. Even today, grasslands continue to be lost to the plow.