Plague is a non-native disease in North America that reduces survival of many mammals. Previous studies have focused on epizootic plague which causes acute mortality events and dramatic declines in local abundance. We know much less about enzootic plague which causes less punctuated reductions in survival and abundance of infected populations. As a result, enzootic plague is much more difficult to detect because changes in population attributes are more subtle and Yersinia pestis prevalence is likely lower relative to epizootic plague outbreaks. The northern Idaho ground squirrel (Urocitellus brunneus) is a threatened species which coexists with Columbian ground squirrels (Urocitellus columbianus) and yellow-pine chipmunks (Neotamias amoenus) throughout their restricted distribution in central Idaho. Columbian ground squirrels and yellow-pine chipmunks are more abundant and widespread than northern Idaho ground squirrels and both are known hosts for plague. Hence, enzootic plague may be one cause of rarity for northern Idaho ground squirrels but its effect on this threatened species has not been evaluated. We conducted three controlled and randomized field experiments to examine the effects of plague in northern Idaho ground squirrels and the two coexisting species: 1) a plague vaccine experiment, 2) a paired flea-reduction experiment, and 3) a non-paired flea-reduction experiment. For Experiment 1, we hypothesized that if enzootic plague is present, vaccinated animals would have higher survival. Furthermore, Experiments 2 and 3 tested the prediction that untreated, control animals should have lower survival than those in areas where fleas are experimentally removed or reduced because fleas are the main vector for plague. In the plague vaccine experiment, vaccinated chipmunks had 4.65% higher apparent survival compared to chipmunks that received a placebo for intervals when the vaccine is believed to be effective. Apparent annual survival increased for all three species on experimental flea-reduction plots compared to non-treated plots for the paired experiment but results were mixed for the non-paired experiment. Taken together, our results suggest that enzootic plague is present and negatively impacting survival of northern Idaho ground squirrels and two coexisting species.