Many factors influence seed choice and handling by rodents. Of them, predation pressure is thought to influence spatial partitioning of patchy environments by rodent species in deserts. In a feeding arena study, we tested how direct and indirect cues of predation influence seed selection and handling behaviors of two Heteromyid rodents, Dipodomys ordii (Ord’s kangaroo rat) and Perognathus parvus (Great Basin pocket mouse). The indirect cue was shrub cover; in each trial half of the arena had sagebrush cover and half had no cover. Direct cues, presented one per trial, were: scent of (1) Canis latrans (coyote) or (2) Vulpes vulpes (red fox), vocalizations of (3) Canis latrans or (4) Asio flammeus (short eared owl), or (5) control with no cues. We offered seeds of two native grasses, Achnatherum hymenoides (Indian ricegrass) and Pseudoroegneria spicata (Bluebunch wheatgrass), and a sterile rye hybrid, Secale montanum (Mountain rye), each in separate plastic trays. D. ordii preferentially harvested A. hymenoides while P. parvus mostly harvested A. hymenoides and S. montanum. No cues affected seed preferences. P. parvus was more likely to cache harvested seeds, whereas D. ordii mostly consumed and/or placed seeds in the larder. However, D. ordii appeared to alter behavior in response to predation cues, placing more seeds in the larder in the presence of some predator cues. Results from our seed fate model suggest that seed harvest and associated seed handing behaviors differ between the species, which could translate into different patterns of plant establishment in natural environments. Our results also suggest that predation pressure has only a minimal impact on the outcome of the seed-seed consumer interaction.