Avian siadenoviruses infect diverse terrestrial and aquatic birds worldwide. Antarctica hosts several avian species that are susceptible to siadenovirus infection, such as penguins and South Polar skuas. However, the presence, diversity, and transmission of these viruses in Antarctic birds are poorly understood due to limited surveillance and sequence data. In this study, we performed a noninvasive surveillance of avian siadenoviruses using fecal samples collected from waterbirds at King George Island (part of South Shetland Islands, Antarctica) from late January to mid-February 2023. Polymerase chain reaction, sequencing, and phylogenetic analysis were used to investigate the occurrence, genetic diversity, and evolutionary relationships of these viruses in this unique environment. The results of these studies confirmed the presence of siadenoviruses in penguins living along the southeastern coast of King George Island. Distinct viral strains, specific to each penguin species studied, were found suggesting limited interspecies transmission and a complex viral ecosystem within Antarctic bird populations. Siadenovirus strains isolated from penguin’s species were genetically distinct from those infecting South Polar skuas. An in silico 3D modeling of hexon proteins from siadenoviruses gathered from gentoo penguins permitted to detect key amino acid substitutions in the FG2 domain that may affect capsid structure and function. The persistent prevalence of siadenoviruses in Antarctica underscores the need for ongoing surveillance to understand the evolutionary dynamics of viruses in this region. This study is the first to noninvasively detect siadenoviruses in Antarctic penguins, opening a new avenue for viral research. This approach not only sheds light on viral dynamics but also contributes to the conservation of Antarctica’s unique wildlife and biodiversity, especially in the face of increasing global warming.