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Currently, there is a dearth of information regarding the status and ecology of bat populations in the Rocky Mountain region of North America due to the scarcity of known hibernacula, which are the primary location for performing population counts in eastern North America. The lack of knowledge and traditional tools required to monitor these populations presents barriers for biologists and land managers tasked with conserving bat species believed to be at risk of extinction or extirpation. Unfortunately, there are no estimates of abundance available for many populations of bats and the absence of locations to monitor populations leaves biologists in many regions without the techniques required to create such estimates. To provide much-needed population ecology data, we designed and built a long-term passive monitoring system capable of continuously monitoring the abundance of little brown myotis (Myotis lucifugus) residing in distinct populations within Yellowstone National Park. To advance our understanding of bat ecology for this region, our monitoring system also assessed roost fidelity, connectivity, and seasonal movements. We subcutaneously implanted high-frequency passive integrated transponders (HF-PIT) into 297 female little brown myotis and installed 8 continuously scanning readers and 45 antennas inside 3 maternity roosts used by distinct populations in the Lamar Valley, Tower Junction, and Mammoth Hot Springs regions of Yellowstone National Park. We recorded 2,929,742 detections of 196 HF-PIT tagged bats (66.0%) between June 2017 and August 2018. We used a mark-resight analysis to quantify abundance based on detections of individually marked bats recorded by high-frequency radio-frequency identification (RFID) readers and counts of bats exiting monitored roosts. From these mark-resight analyses, we estimated the pre-parturition size of the Mammoth population to be 847 (95% CI = 749-987; SE 59.8) in 2017, and 836 (95% CI = 722-989; SE 67.3) in 2018. The Lamar Valley population was estimated to consist of 208 (95% CI = 198-222; SE 6.2) bats in 2018. Population estimates were not possible at Tower Junction, but RFID readers showed that only a single HF-PIT tagged bat moved among these three roosts. Population estimates at Mammoth and Lamar reflect roost availability, as 258 and 25 potential roosts were available within 1 km of RFID-monitored in Mammoth and Lamar Valley, respectively. Although roost availability and populations were larger in Mammoth, roost fidelity was similar between the two sites, with bats detected in the monitored roosts on 36.5% of days in Mammoth and 31.4% of days in Lamar Valley. Combining traditional emergence counts with RFID technology and mark-resight analyses presents a novel approach to estimating bat populations during summer, which has long vexed researchers. While especially useful for regions lacking caves, and thus any traditional method to census populations, these techniques provide a vital opportunity to advance knowledge of bat ecology nationwide during a season rarely studied.