This dataset supports a study investigating populations of the common bottlenose dolphin (Tursiops truncatus) across the Mediterranean Sea and adjacent North Atlantic using high resolution genomic markers (RADseq) and stable isotope analyses t. Samples included archived DNA that had been used in previous studies, as well as newly collected samples. Genomic libraries for double-digest restriction associated DNA were constructed, sequenced on three lanes of an Illumina HiSeq 2500 sequencer. High resolution genomic data and broad geographic sampling revealed patterns of structure not previously identified, and integration with stable isotope data suggests that prey choice varies across this region. The regional habitat within and beyond the Mediterranean Sea is structured with ocean frontal systems including thermal and halocline transitions, several of which show alignment with genetic transitions within our data. Our data help to distinguish among possible drivers of population differentiation for a marine predator that has the potential for long-distance dispersion.