The Buccal Micronucleus Cytome (BMCyt) assay is a relatively non-invasive method successfully applied to evaluate genomic damage for biological monitoring of human populations exposed to various mutagenic and carcinogenic compounds. This paper presents a protocol developed to apply the buccal micronucleus assay to wild mammal species during field or management activities. We applied the BMCyt to one population of Eastern grey squirrels (Sciurus carolinensis, n = 37) and one of wild boars (Sus scrofa, n = 41) living in anthropized and natural areas, respectively. Micronuclei, nuclear buds, and other nuclear abnormalities, e.g. binucleated, Kidney-shaped nucleus, karyorrhexis, cell with condensed chromatin, pyknotic and karyolysis, were recorded. The frequencies of micronuclei and nuclear buds were respectively 0.51±0.60 and 1.29±1.08 for wild boars and 0.16±0.37 and 0.57±0.73 for grey squirrels. Sex, age classes and body weight had generally no effects on the frequencies of genomic damages, except for a limited effect of weight on broken eggs and karyolitic cells in grey squirrels and of sex in of condensed chromatin in wild boars. In conclusion, the results of this study indicate that buccal mucosa is a sensitive site for detecting micronuclei and other nuclear abnormalities and that the protocol used in this paper may represent a valuable tool to evaluate the genomic damage in wild species living in both anthropized and natural areas.