Several studies published in the last 20 years have shown that complex communities of microbes, known as the microbiome, inhabit the different sites of the human and animal body. Due to these new concepts, Lederberg coined the term microbiome in 2000, describing a more “ecologically-informed metaphor” to better understand and describe the relationship between human hosts and their microbes. This article synthetically presents the results of research on the skin microbiome in animals in physiological states and in periods of health imbalance. Small number of studies that describe the skin microbiota in animals have been published to date. These have included only limited numbers of animals, rendering them rather descriptive, currently. So far, the bacterial skin microbiome has been studied in dogs, cats, cattle, sheep, and amphibians. In contrast, the skin mycobiome has been defined only in dogs and cats. The analysis of the literature made it possible to draw a conclusion that the skin microbiome has unique composition: it varies across body areas and a remarkable variability is seen across different individuals.