Here we review the knowledge about skin microbiomes in amphibians accumulated over the last two decades and the evidence regarding the protective role of skin bacteria. Amphibians all over the world are declining because of several factors, including chytridiomycosis disease caused by the fungal pathogens Batrachochytrium dendrobatidis and B. salamandrivorans. In this context, the antifungal capacities of many bacteria living symbiotically on amphibian skin, which have been described both in vitro and in vivo, are important in disease prevention. We discuss the major factors influencing amphibian skin bacterial communities, the fungal component of the amphibian skin microbiome, and the potential use of antifungal bacteria as probiotics. The structure of amphibian skin microbial communities is influenced by host-specific microhabitat, biogeographic, and climatic factors, but the functional aspects of these microbiomes and how these nested factors modulate skin microbial functions remains largely unexplored. However, the field has grown considerably, and recent technologies have prompted the exploration of exciting new questions aimed at providing more detailed knowledge about the ecology of amphibian–microbial symbioses and the precise role of the skin microbiome in protecting host amphibians against emerging diseases.