Understanding the microbiota of wild animals can contribute to the monitoring of population health or habitat changes. The skin microbiota of fallow deer remains poorly characterized and represents a gap in current veterinary microbiology research. The aim of this study was to analyse skin microbiota of fifteen clinically healthy fallow deer using next-generation sequencing. Genomic DNA was extracted from superficial skin swabs collected from three anatomical sites per individual (n = 45 samples) and sequenced targeting the V3-V4 region of the bacterial 16S rRNA gene using Illumina sequencing. The skin microbiota of fallow deer was highly diverse, with a broad range of bacterial taxa detected across samples. The most abundant genus was Sphingomonas, followed by Enhydrobacter, Chryseobacterium, Corynebacterium, Pseudomonas, Flavobacterium, Sporosarcina, and Staphylococcus. Significant differences in alpha diversity were detected between male and female fallow deer. Beta diversity analysis revealed significant differences in community composition according to sex and age, whereas no significant differences were observed among sampling locations or skin sites. To our knowledge, this is the first study to describe the skin microbiota composition of fallow deer, providing baseline data for future comparative and ecological microbiota studies in wild ruminants.