Small mammals use plant species for gathering food resources and for shelter. Preferences for certain plant species are related to nutritional restrictions and behavioural patterns, which could be altered in the presence of an infectious disease. Several native small mammals are part of the wild cycle of the protozoan Trypanosoma cruzi, responsible for Chagas disease in humans. This is a vector-borne disease transmitted by insects of the subfamily Triatominae. We examined the effect of T.cruzi infection status on the use and preference patterns of shrub species by two native rodent species: Octodon degus and Phyllotis darwini. This study was conducted during four sampling years (2010-2013) in a hyper-endemic zone of Chagas disease located in a semiarid Mediterranean ecosystem. We captured individuals of 599 O.degus and 575 P.darwini (89% of the total captures), which were related to nine shrub species and examined for T.cruzi infection. In a community-level analysis, infected and non-infected O.degus used individual shrub species within the shrub community significantly non-randomly relative to their availability; the same pattern was detected for non-infected P.darwini individuals, whereas infected individuals used the shrub community according to the abundance of each shrub species. Examining individual preferences, both rodents showed a strong preference for Flourensia thurifera and Colliguaja odorifera regardless of their infection status. Preferences for specific shrub species were variable among years, showing a core' of preferred shrub species and variable levels of use of the remaining ones. Our results show that T.cruzi infection in wild small mammals can modify habitat use patterns and preferences for certain shrub species, probably affecting processes acting at community level.