It is intuitive that the same vectors that introduce species to new ranges could move them amongst native populations, but whether human-mediated dispersal impacts evolutionary trajectories has been difficult to address because gene flow via human-mediated dispersal is difficult to distinguish from gene flow via natural dispersal when both occur simultaneously. Here, we investigate the effects of human-mediated dispersal by exploiting a system where the primary vector was once extensive but has since ceased. From the 10th -19th Centuries, ships in the North Atlantic exchanged sediments dredged from the intertidal for ballast, which ended when seawater ballast tanks were adopted. We investigate genetic patterns from RADseq-derived SNPs in the amphipod Corophium volutator (n=121 4870 SNPs) and the annelid Hediste diversicolor (n=78 3820 SNPs), which were introduced from Europe to North America, have limited natural dispersal capabilities, are abundant in intertidal sediments, and absent from modern water ballast tanks. We detect similar levels of genetic subdivision amongst introduced North American populations as amongst native European populations, despite the longer evolutionary history in Europe. Phylogenetic networks and clustering analyses reveal population structure between sites, extensive phylogenetic reticulation and a lack of phylogeographic structure between populations within ranges, and phylogenetic splits between European and North American populations. These patterns are consistent with the hypothesis that human activity eroded ancestral phylogeographic structure between native populations, but was insufficient to overcome divergent processes between naturalized populations and their sources. Our results suggest that human activity may alter species’ evolutionary trajectories on a broad geographic scale via regional homogenization and global diversification, and that movement within native ranges may in some cases preclude historical inference from genetic data by eroding ancestral phylogeographic structure.