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 individuals 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 fastâevolving immune genes, of which tollâlike receptor (TLR). In this study, we examined the genetic diversity at 14 TLR loci across P.ânobilis, Pinna rudis and P.ânobilisâĂâP.ârudis hybrid genomes, collected at four physically distant regions, that were found to be either resistant or sensitive to the parasite H.âpinnae. We report a high genetic diversity, mainly observed at cell surface TLRs compared with that of endosomal TLRs. However, the endosomal TLRâ7 exhibited unexpected level of diversity and haplotype phylogeny. The lack of population structure, associated with a high genetic diversity and elevated dN/dS ratio, was interpreted as balancing selection, though both directional and purifying selection were detected. Interestingly, roughly 40% of the P.ânobilis identified as resistant to H.âpinnae were introgressed with P.ârudis TLR. Specifically, they all carried a TLRâ7 of P.ârudis origin, whereas sensitive P.ânobilis were not introgressed, at least at TLR loci. Small contributions of TLRâ6 and TLRâ4 singleânucleotide polymorphisms to the clustering of resistant and susceptible individuals could be detected, but their specific role in resistance remains highly speculative. This study provides new information on the diversity of TLR genes within the P.ânobilis species after MME and additional insights into adaptation to H.âpinnae that should contribute to the conservation of this Mediterranean endemic species.