<p>Penguins are central to Antarctic ecosystems, serving as integral components of the food web and shaping diverse bacterial communities, especially in ornithogenic soils. This systematic review synthesizes current knowledge on the bacterial diversity and community composition associated with Antarctic penguins, while exploring their potential biotechnological applications. It highlights interspecific differences in microbial communities driven by factors such as diet, habitat, and host physiology. We also discuss how these microbes can serve as indicators of environmental change and contribute to penguin health. Furthermore, we examine their promise in biotechnology, including the discovery of novel antimicrobial compounds and enzymes. By underscoring the ecological and applied significance of these microbes, this review aims to advance understanding of penguin-associated bacterial diversity in the face of accelerating climate change.</p>