Crustose coralline algae (CCAs) are one of the main components of coralligenous, one of the most diverse marine habitats in the Mediterranean Sea. Beyond their role as ecosystem engineers, certain CCAs have been shown to favor the settlement of gorgonian larvae, an important capacity in the context of the restoration of these species. Similarly to other species, CCAs live associated to symbiotic microorganism forming a holobiont. Despite their ecological importance and vulnerability to climate change, Mediterranean CCA holobionts have been understudied in terms of taxonomy and microbiome. Using electron microscopy and barcoding techniques, we identified Lithophyllum stictiforme complex and the genus Mesophyllum, two widespread CCA morphotypes from the Western Mediterranean Sea, which are often found in close proximity with gorgonians. 16S rRNA amplicon sequencing revealed that these two CCAs harbor distinct and diverse bacterial communities. Bacterial communities also differ between thalli of the same CCA morphotype, showing greater similarity between neighbor thalli, suggesting that exogenous factors acting at small spatial scale may influence bacterial composition. The predominance of bacterial sequences affiliated to the Blastopirellula genus and Pir4_lineage of the phylum Planctomycetes in all CCA individuals examined is noteworthy. These bacterial groups have been hypothesized to promote tropical coral larvae settlement, raising the possibility of a similar positive interaction between CCAs and Mediterranean coral larvae.