Seed predation and rodent foraging behaviors depend on frequency of available seeds and seed traits. However, the interaction of frequency of seed availability and seed traits adds a new level of complexity to granivore–seed dynamics. We conducted experiments with eastern gray squirrels (Sciurus carolinensis) designed to elucidate the frequency × trait interaction. We hypothesized that frequency-dependent caching should occur only among pairs of seeds that are relatively similar in attributes that affect their perceived value as a storable food item. We also tested whether caching decisions were dependent on seeds already cached, a variable rarely considered in seed dispersal studies. Frequency-dependent seed caching occurred when seeds of relatively similar value (Juglans regia and Castanea mollissima) were paired. For this seed pair, caching decisions by S. carolinensis were dependent on seeds already cached such that squirrels tended to cache seeds that were either rare in the environment or in the cache. When seeds of very different caching values were paired (Juglans nigra and Corylus americana), a strong preference for the high-value seed was observed, but no frequency-dependent selection. We conclude that in pairings of seeds of differential caching value, the highly preferred seed is cached regardless of frequency of availability. In contrast, when seeds of similar value are paired, rarer (more common) seeds are cached at a higher (lower) rate than expected, and this behavior potentially stabilizes seed survival across available seed types leading to increased tree diversity. Our results indicate that caching of seeds by squirrels, and by implication recruitment of seedlings into plant populations, is likely driven by complex interactions between the relative frequency of seeds and their traits. We expect similar patterns to occur in any system in which foragers select among resource types that vary in perceived value.