The Iron Age saw the expansion of Phoenician and Greek colonies across the Mediterranean and the rise of Carthage as the major maritime power of the region. These events were facilitated by the ease of long-distance travel following major advances in seafaring. From the archaeological record, we know that trade goods and materials were moving across great distances in unprecedented quantities, but it is unclear how these patterns correlate with human mobility. To investigate population mobility and interactions directly, we sequenced the genomes of 30 ancient individuals from Carthaginian and Etruscan port cities around the central Mediterranean. We observe high heterogeneity at these sites in Tunisia, Sardinia, and central Italy. At all three locations there is a meaningful contribution of autochthonous populations (from North Africa, Sardinia, and Bronze Age Italy, respectively), as well as many individuals with ancestry from other parts of the Mediterranean region, highlighting the extreme interconnectedness of populations in the Iron Age Mediterranean. By studying these trans-Mediterranean neighbors together, we explore the complex interplay between local continuity and mobility that shaped the Iron Age societies of the central Mediterranean.