Fine-scale habitat information can provide insight into species occupancy and persistence that is not apparent at the landscape-scale. Such information is particularly important for rare species that are experiencing population declines, such as the threatened Yosemite Toad (Anaxyrus canorus). Our study examined differences in physical characteristics of occupied and unoccupied toad breeding pools within meadows, and then used a logistic regression model to evaluate if occupancy was related to the physical microhabitat variables. We found that occupied pools on average were deeper by 0.7 cm, warmer by 3°C, and had 50% more surface water along the short axis of the pool. Mean water depth, mean water temperature, the amount of surface water in the pools, mean detritus depth, and mean vegetation height were significant predictors of toad occupancy. Despite variation in larger-scale environmental conditions such as yearly winter snow cover and precipitation, occupancy was not related to individual years and microhabitat requirements for toad occupancy appear to be relatively constant. Pools were very shallow water bodies (mean depth 4.35 cm for occupied pools), and differences in physical microhabitat variables for suitable breeding sites were small but significant. This underscores the importance of fine-scale habitat information for breeding and reproduction of A. canorus, and for species persistence and management.