Human activities are increasingly causing anthropogenic hybridization in urban habitats. Hybridization between the invasive mussel Mytilus galloprovincialis and its 2MY-divergent native congener, M. edulis, resulted in the emergence of a distinct dock mussel ecotype restricted to certain commercial ports of coastal cities. The genetic make-up of dock mussels was previously found to be consistent across individuals and populations, with an invasive:native ancestry ratio of approximately 3:1. We screened over 2000 mussels using a KASP multiplex genotyping approach to select 320 dock mussels from 8 ports for which we inferred local ancestry variation across the genome using a medium density 60K SNP array. We found dock mussels in newly studied ports and differences in average ancestry proportion between the northernmost and southernmost port populations. Contrary to common expectations, the dock mussel genome was found fully admixed, without there being a single desert or a single peak of ancestry fixation anywhere. Two peaks of high native parent ancestry suggest adaptive introgression for locally selected genes. However, our results are mainly consistent with a highly multigenic fitness landscape model, which predicts selection for increased ancestry heterozygosity genome-wide, and hybrids overshoting the fitness of the fittest parental lineage. Overall the landscape of ancestry detected within the dock mussel ecotype genome was likely shaped by intricate mechanisms involving polygenic selection processes in interaction with recombination and demography.