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Kangaroo rats participate in an ancient symbiosis with fungi that colonize their seed caches. This paper reports on four yr of intensive sampling in central New Mexico to identify the fungi associated with the banner-tailed kangaroo rat and to determine the factors that influence that fungal community. Although more than 80 molds were recovered from the rodents, a much smaller set of molds, including a new species of Penicillium, dominate this system. Factors affecting the number of colonies, number of species, or identity of fungal species recovered in samples included moisture conditions around the time of sampling, sample type (cheek-pouch or hind foot), and rodent traits such as age, sex, reproductive status, and mobility.