As the first barrier to environmental exposures, human skin has developed an integrated immune system to protect the inner body from chemical, physical or microbial insults. Microorganisms inhabiting superficial skin layers are known as skin microbiota and include bacteria, viruses, archaea and fungi. The microbiota composition is crucial in the instruction and support of the skin's immune system. Changes in microbiota can be due to individual, environmental or behavioral factors, such as age, climate, hygiene or antibiotic consumption, which can cause dysbiosis. The contribution of skin microbiota to disease development is known in atopic dermatitis, where there is an increase in Staphylococcus aureus. Culture-independent studies have enabled more accurate descriptions of this complex interplay. Microbial imbalance is associated with the development of various diseases. This review focuses on microbial imbalances in acne vulgaris and rosacea.