The brown alga Padina (Dictyotales, Ochrophyta) is found worldwide, predominantly in tropical to subtropical waters. Due to their similar appearances, distinguishing between different Padina species is challenging. Historically, morphological characteristics such as the degree of calcification and thallus color were the primary methods for identifying and differentiating Padina species, which often led to misidentifications. The advent of molecular-aided taxonomic identification has allowed for more reliable classification of species. In this study, we utilized sequence comparisons of two genes, the chloroplast rbcL and the mitochondrial cox3, to identify Padina specimens collected from six sites along the Israeli coast of the Mediterranean Sea. Our results revealed the presence of three distinct Padina species: P. pavonica, P. boergesenii, and P. pavonicoides, the latter of which has not been previously reported in this region. Additionally, we observed that the distribution of these species along the shores was not homogeneous: P. pavonica was predominantly found along the northern shores, while P. boergesenii was mostly found along the southern shores.