Sensitive skin (SS) syndrome is a globally widespread, self-diagnosed discomfort characterized by subjective complaints. Although the skin microbiome is considered important in skin health, the relationship between the skin microbiome and skin sensitivity is still unknown. Here, we aimed to (i) investigate whether the microbiome and mycobiome of SS are distinct from those of non-sensitive skin (NS), and (ii) define the characteristics of the skin microbiome associated with skin sensitivity. A total of 42 Korean women subjects were recruited (SS, n = 23; NS, n = 19) and the microbiome/mycobiome of their right facial cheeks were analyzed. We identified the differential microbiome and mycobiome structures between SS and NS. The mycobiome of SS was more phylogenetically diverse than that of NS. Lactobacillus and Mucor racemosus were more abundant on SS than NS, whereas Malassezia restricta was less abundant. Interestingly, both skin microbiome and mycobiome varied according to the perceived skin sensitivities of the subjects. This study suggests that the skin microbiome and mycobiome are associated with skin sensitivity. Accordingly, it lays the foundation for developing microbiome-based cosmetics or remedies for individuals suffering from SS syndrome.