The fan mussel Pinna nobilis is currently on the brink of extinction due to a multifactorial disease mainly caused to the highly pathogenic parasite Haplosporidium pinnae, meaning that the selection pressure outweighs the adaptive potential of the species. Hopefully, rare specimens have been observed somehow resistant to the parasite, stretching the need to identify the traits underlying this better fitness. Among the candidate to explore at first intention are fast evolving immune genes, of which toll-like receptor (TLR). In this study, we examined the genetic diversity at 14 TLR loci across Pinna nobilis, Pinna rudis and Pinna nobilis x Pinna rudis hybrid genomes, collected at four physically distant regions, that were found to be either resistant or sensitive to the parasite Haplosporidium pinnae. We report a high genetic diversity, mainly observed at cell surface TLRs compared to that of endosomal TLRs. However, the TLR-7 and TLR-1 exhibited unexpected level of diversity and haplotype phylogeny, respectively. The lack of population structure, associated with a high genetic diversity and elevated dN/dS ratio were interpreted as balancing selection, though both directional and purifying selection were detected. Overall, we observed small contributions of putatively selected SNPs involved in the resistance. However, the most contributing SNPs were carried by two TLR-6 loci and might be used as potent biomarkers of distinguish between resistant and sensitive P. nobilis individuals. Moreover, more than 10% of P. nobilis individuals were found introgressed with P. rudis. Noteworthy, all introgressed P. nobilis observed as resistant to H. pinnae carried a TLR-7 of P. rudis origin. This study contributes to the ongoing efforts towards conservation carried out to prevent from extinction this Mediterranean endemic species.