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Conservation of populations in fragmented habitats is often based on spatially realistic metapopulation theory, which predicts negative relationships between patch extinction and area and patch colonization and isolation. Cost-distance metrics have been developed to integrate habitat quality into measures of connectivity, and thus may improve predictive power of the area-isolation paradigm. Few studies use empirical data to compare predictive performance of complex cost-distance metrics to simple metrics relying on Euclidean distances. We used 3 years of presence–absence data to examine relative influence of habitat quality, habitat area, and connectivity on occupancy and extinction rates for Poliocitellus franklinii (Franklin’s ground squirrel), a rare grassland species of conservation concern. We calculated connectivity using nearest-neighbor (NN) and incidence function model (IFM) metrics based on Euclidean and cost-distances. Habitat quality, area, and connectivity were all positive predictors for occupancy, but only isolation was a positive predictor of extinction. P. franklinii does not appear to be a tallgrass prairie obligate, but the species distribution is limited by isolation of suitable grassland habitat. A simple NN metric measuring Euclidean distance between a target area and nearest occupied source outperformed IFM (Euclidean and cost-distance) in predicting occupancy and extinction for P. franklinii. Although NN metrics are criticized for considering only the contribution of the source nearest to a target, this simplicity may be acceptable when measuring connectivity for rare species with few occupied habitat patches within dispersal distance.