As global biodiversity continues to reduce at an alarming rate, threatened species are increasingly being brought under intensive management or into captivity. However, current conservation management programmes are often impeded by poor animal health and low reproductive success. Microorganisms play vital roles in the growth and maintenance of healthy multicellular organisms, including neurological and immune system development, gut nutrition, and pathogen defence. The microbiome refers to the vast community of microorganisms, and their collective genes, that live on and within a host organism. An imbalance or breakdown of the microbiome may in some cases be associated with severe negative health consequences for the host. Factors such as habitat degradation and transition into captive breeding programmes can significantly alter the microbiome of threatened species, though the effects of such microbial community changes on health, fitness and ultimately survival of the animals remain poorly understood. This perspective article collates important microbiome research in threatened animals from around the world to make a case for the inclusion of microbial research in modem conservation practice.