Microbiome research is revealing the profound effects that microbial inhabitants can have on their animal hosts. Recent and rapid advances in sequencing technologies have allowed biologists to characterise the microbial constituents of a variety of host organisms, giving greater insights into these intimate relationships than ever before. For many animal species, microbiomes serve as an interface between host and environment, with associated microorganisms playing functional roles in nutrition, immunity, reproduction, and even behaviour. In this Review, we offer a brief overview of microbiome research methodology before summarising previous and ongoing research into the microbiomes of native New Zealand animals. Our unique endemic fauna, evolved during tens of millions of years of geographic isolation, offers exciting opportunities for microbiome research across a range of diverse taxa and we highlight key findings of relevant studies. Moreover, while recognising the crucial role that 16S rRNA gene sequencing plays in microbiome research, we conclude the Review with a look beyond 16S and consider what other technologies can bring to this field. We encourage further investigation into the functional roles of microbial species across a broader range of host-animal taxa across New Zealand, both in wild and captive states.