Oral vaccination against Yersinia pestis could provide a feasible approach for controlling plague in prairie dogs (Cynomys spp.) for conservation and public health purposes. Biomarkers are useful in wildlife vaccination programs to demonstrate exposure to vaccine baits. Rhodamine B (RB) was tested as a potential biomarker for oral plague vaccination because it allows nonlethal sampling of animals through hair, blood, and feces. We found that RB is an appropriate marker for bait uptake studies of <60 days in black-tailed prairie dogs (C. ludovicianus) when used at concentrations <0.5% of bait mass dosed to deliver >10 mg RB per kg target animal mass. Whiskers with follicles provided the best sample for RB detection.