Scientists collect fleas (Siphonaptera) to survey for Yersinia pestis, the bacterial agent of plague. When studying fleas parasitizing prairie dogs (Cynomys spp.), two primary methods are used: (1) combing fleas from live-trapped prairie dogs and (2) swabbing fleas from burrows with cloth swabs attached to metal cables. Ideally, burrow swabbing, the cheaper and easier method, would explain flea burdens on prairie dogs and provide reliable information on plague prevalence. In a linear regression analysis of data from 1-month intervals (June–August 2010–2011) on 13 colonies of black-tailed prairie dogs (Cynomys ludovicianus, BTPDs) in New Mexico, flea abundance on swabs explained 0–26% of variation in BTPD flea burdens. In an analysis of data (May–August 2016) from six colonies of BTPDs in Montana, flea abundance on swabs explained 2% of variation in BTPD flea burdens. In an analysis of data from a short-term interval (July 23–27, 2019) on four colonies of BTPDs in Montana, flea abundance on swabs explained 0.1% of variation in BTPD flea burdens. In an analysis of data from 1-week intervals (August–October 2000) on four colonies of white-tailed prairie dogs (Cynomys leucurus, WTPD) in Utah, swabbing data explained 0.1% of variation in WTPD flea burdens. Pools of fleas from two WTPD colonies were tested for Y. pestis by mouse inoculation and isolation; 65% from WTPDs tested positive, whereas 4% from burrows tested positive. Data herein also show that results from burrow swabbing can misrepresent flea species composition and phenology on prairie dogs. Burrow swabbing is useful for some purposes, but limitations should be acknowledged, and accumulated data should be interpreted with caution.