We assess and compare prokaryote communities from four sponge species and the surrounding seawater collected in two South Shetland Islands and at two locations in the Antarctic Peninsula separated by ca. 670 km. We sought to answer the following questions: 1) How is the diversity and microbial community composition associated to Antarctic marine sponges, compared to the surrounding seawater? 2) Is there a core-microbiome associated to them? 3) Are these communities host-specific and consistent over a geographic scale? This is one of the first reports that used high throughput sequencing to unravel the composition and diversity of symbiotic microbial communities associated to Antarctic marine sponges.