Contrasting patterns of population structure and historical dynamics between two octopus species, Eledone moschata (Lamarck, 1798) and E. cirrhosa (Lamarck, 1798), in the Mediterranean basin

This dataset contains genome-wide SNP data (VCF files) and mitochondrial COI sequences used to investigate genetic diversity, population structure, and demographic history of two closely related octopus species, Eledone moschata and Eledone cirrhosa, across the Mediterranean Sea and adjacent Northeast Atlantic Ocean. The genomic data were generated using ddRAD sequencing and include multiple SNP datasets for both species, enabling analyses of population differentiation, connectivity, and gene flow. The dataset supports findings of contrasting population structures between the two species, with restricted connectivity in E. moschata and high connectivity within Mediterranean populations of E. cirrhosa, alongside distinct Atlantic–Mediterranean differentiation.