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In agricultural habitats, diets and trophic positions of syntopic granivorous small mammals are not known sufficiently. Agroecosystems may be quite complex isotopically and the most complex situation concerns the nitrogen-15 isotope as <i>δ</i>¹⁵N values are influenced by many internal and external fluxes. We analysed the isotopic niches of striped field (<i>Apodemus agrarius</i>), yellow-necked (<i>Apodemus flavicollis</i>), and harvest (<i>Micromys minutus</i>) mice living sympatrically and syntopically in apple and plum orchards, raspberry and currant plantations, and nearby meadows that were used as control habitats. Carbon (<i>δ</i>¹³C) and nitrogen (<i>δ</i>¹⁵N) stable isotope ratios from hair samples were used as a proxy for their diet. As the main hypothesis, we expected differences in the isotopic niches of these three species, minimising interspecific competition. All species were fully separated according to <i>δ</i>¹⁵N values, presuming different amounts of food of animal origin in their diet. The separation of species according to <i>δ</i>¹³C was not expressed in all habitats. The core dietary niches of these species were fully separated in the apple orchards and raspberry plantations. Intraspecific differences of the isotopic niche were not present in any of the three species: that is, resources were equally used by males and females, adults, subadults, and juveniles.