Unravelling the history and pathways of range-shifting species is key for understanding their past, current, and future distributions. Anthropogenic transport of species alters natural dispersal patterns and directly affects population connectivity. Studies have suggested that high levels of anthropogenic transport homogenise patterns of genetic differentiation and blur invasion routes. However, empirical evidence of these effects remains elusive. We compared two marine non-indigenous species (Microcosmus squamiger and Ciona robusta) to examine how anthropogenic transport affects our ability to reconstruct colonisation pathways using genomic data. We first investigated shipping networks from 1750 onwards, cross-referencing these with regions where the species have historical records and inferred that each species has been affected by different levels of anthropogenic transport. We then genotyped thousands of single nucleotide polymorphisms from 280 M. squamiger and 190 C. robusta individuals collected across the species’ ranges and reconstructed invasion routes. Dissimilar invasion routes were resolved, yet the genomic signatures of each species could be elucidated irrespective of levels of anthropogenic transport. Thus, inferences of invasion routes using genomic data were not obscured by the history and intensity of anthropogenic transport of species. We conclude that high-resolution genomic data are a robust tool for informing management decisions on range-shifting species.