Amoebae are protists that have complicated relationships with bacteria, which cover the whole spectrum of symbiosis. Amoeba-bacteria interactions contribute to the study of predation, symbiosis, pathogenesis, and human health. Given the complexity of their relationships, it is necessary to understand the ecology and evolution of their interactions. In this paper, we provide an updated review of the current understanding of amoeba-bacteria interactions. We start by discussing the diversity of amoebae and their bacterial partners. Besides, we define three types of ecological interactions between amoebae and bacteria and discuss their different outcomes. Finally, we focus on the implications of amoeba-bacteria interactions on human health, horizontal gene transfer, drinking water safety, and the evolution of symbiosis. In conclusion, amoeba-bacteria interactions are excellent model systems to investigate a wide range of scientific questions. Future studies should utilize advanced techniques to address research gaps such as detecting hidden diversity, lack of amoebae genome, and the impacts of amoeba predation on the microbiome.