Crustose coralline algae (CCAs) are key components and primary builders of coralligenous reefs, which are among the most biodiverse marine habitats in the Mediterranean Sea. Beyond their structural role, CCAs play a crucial role in promoting larval settlement in a variety of invertebrate species, including corals. In addition, CCAs form complex holobionts through association with symbiotic microorganisms that can modulate their ability to induce larval settlement and provide information on their health status. Despite their ecological significance and potential for biomonitoring, the microbial communities associated with Mediterranean CCA holobionts remain largely understudied. Using electron microscopy and barcoding techniques, we identified Lithophyllum stictiforme complex and Macroblastum dendrospermum, two widespread CCAs from the Western Mediterranean Sea, living in sympatry with gorgonians. The 16S rRNA gene amplicon sequencing revealed that these CCAs host distinct and diverse bacterial communities, even among thalli of the same species, with closer thalli showing more similar bacterial assemblages. Our findings suggest that the primary factors influencing the bacterial communities include the host genotype, local environmental conditions at the individual thallus scale, and possible horizontal transfer between adjacent thalli. The predominance of bacterial sequences affiliated to the Blastopirellula genus and Pir4_lineage in phylum Planctomycetes across all CCA individuals examined is noteworthy. These bacterial groups have been hypothesized to promote coral larvae settlement in tropical regions, raising the possibility of a similar facilitative interaction between CCAs and Mediterranean coral larvae.