The hydrothermal springs (HTSs) are unique environments characterised by the emergence of geothermally heated groundwater that often releases large amounts of dissolved minerals. Despite interest in HTSs, the microbial composition of these sites remains largely under-explored, particularly concerning the interactions between marine invertebrates and microorganisms. As an example, the shallow HTSs of Trapani (West coast of Sicily, Italy) maintain a constant temperature of 31 °C throughout the year and two invertebrates and are inhabited by the nudibranch Peltodoris atromaculata (P. atromaculata) and the sponge Petrosia ficiformis (P. ficiformis). This study aimed to analyse the bacterial communities associated with the sponge P. ficiformis and the mantle and gut of P. atromaculata. Our results, based on Next-Generation sequencing of the bacterial marker gene (16S rDNA), revealed that the bacterial communities associated with the sponge P. ficiformis and the mantle of P. atromaculata are strikingly similar, suggesting a shared bacterial community, while also exhibiting distinct bacterial differences. However, signatures of bacterial families were found in the gut and mantle of P. atromaculata. These findings shed light on the bacterial composition of the nudibranch P. atromaculata and the sponge P. ficiformis, both considered bioindicators of environmental conditions and highlight the importance of investigating the microbial biodiversity in these peculiar environments to be preserved at every taxonomic level. Additionally, to date, we have provided a brief introduction to understanding the role of host-bacteria interactions in marine invertebrates and these unique environments in shaping entire communities.