The number of microbes in the stomach and gut of animals is huge, and various microbial communities constrain each other. Those microbes co-evolve with their hosts. The Southern Ocean, as a huge biological resource bank, supports a large number of animals. The diversity and specialty of its living environment make the gut microbes of animals extremely special. The gut microbial community has evolved to adapt to various nutritional life styles of host species. From the perspective of representative Antarctic organisms in different trophic levels, this review summarizes gut microbe composition of those species. The advantages and disadvantages of research approaches related to those studies are also analyzed. This review is expected to reveal the relationship between the gut microbes and their hosts, and further to provide a reference for more effective development and utilization of microbial resources in this region.