The pygmy rabbit (Brachylagus idahoensis) is a cryptic, burrowing lagomorph of conservation concern for which an efficient method to monitor populations is needed for conservation planning. We developed an index of abundance based on density of active burrow systems at 7 sites (57.2–118.5 ha) in east central Idaho. We conducted censuses of burrow systems and used mark-resight surveys of 80 radio-collared individuals to estimate density of rabbits. At 5 sites, we also used a second method to estimate rabbit numbers based on presence of tracks in snow around burrow systems. We evaluated patterns of burrow use by individuals and examined the relationship between vegetation structure and density of rabbits. Density of active burrow systems varied from 0.19 to 3.46 per ha, and density of rabbits ranged from 0.02 to 0.46 per ha. Number of burrow systems used by individuals increased with density of available burrows, which supported a nonlinear relationship between abundance of burrows and rabbits. Population density increased curvilinearly with density of active burrows accounting for >75% of the variation (r2 = 0.79) in population estimates across sites. We documented a positive relationship between visual obstruction of vegetation and density of rabbits across 6 of the study sites. Our results suggest that density of burrows can serve as an index for monitoring changes in abundance of pygmy rabbits in east central Idaho and that this index also might be useful for monitoring changes in relative abundance over time at other locations. To assess abundance at larger spatial scales or across different regions, the index should be calibrated under regional conditions and site-level covariates should be evaluated.