Animals provide a diverse array of habitats for microorganisms to colonise, and virtually all animals form symbiotic relationships with one or more microbial species. One group of “host” animals that houses a particularly diverse and abundant community of bacteria and other microorganisms is the marine sponges. Microbes comprise as much as 40% of “sponge” volume and can contribute significantly to host metabolism. The remarkable diversity and host specificity of these symbionts, coupled with the presumed ancientness of the sponge-microbe association, makes sponges an important system for the study of marine host-microbe interactions. I will present my group’s research on the microbial ecology of sponges, emphasizing how recent advances in DNA sequencing technologies have provided exciting new insights into how these complex associations are maintained. I will also touch upon some of our recent research into the microbiota of other host organisms, including the critically endangered New Zealand kakapo parrot and aspects of the human microbiome.