Pinna nobilis (lat. Pinna nobilis) is endemic to the Mediterranean Sea, where it is the largest bivalve whose height can reach up to 1 m. It is most often found stuck vertically on the sandy-mud bottom, where it inhabits meadows of Seagrass (Posidonia oceanica and Cymodocea nodosa). It has an important ecological role because it is a filter-feeder organism and contributes to water transparency. Its shells serve as a hard surface that is colonized by various epibionts. It has been on the list of endangered species since 1992, and its number decreased drastically after the Mass Mortality event started in the fall of 2016. In this work, 47 DNA sequences were analyzed to gain insight into the population genetics of the species, and the molecular marker Cytochrome Oxidase I was used, one of the most widespread marker used for evolutionary analyses. The sequences were processed in the MEGA-X software package. Sampling was carried out between 2018 and 2019 at 7 locations along the Croatian coast and the islands of the Adriatic Sea. For the most part, it is evident that most of the samples are genetically identical, that is, among the 47 analyzed samples, 17 different haplotypes were found, with the most numerous haplotype being found in 20 samples and present in all 7 sampled locations. A total of 32 point mutations were detected, of which only one was a missense mutation, while the rest were silent mutations. Likewise, by comparing our research groups, using BLAST, and other populations across the Mediterranean, as many as 76% of our haplotypes, in the full length of 553 nucleotides, are identical to already published sequences sampled across the Mediterranean.