Marine organisms show population structure at a relatively fine spatial scale, even in open habitats. The tools commonly used to assess subtle patterns of connectivity have diverse levels of resolution. We have assessed the discriminatory power of genetic markers and otolith shape to reveal the population structure of the common sole (Solea solea), living in the Eastern English Channel stock off France and the UK. The aims were to (i) inform the short and long-term population structure by comparing genetic and otolith shape approaches, and (ii) combine the tracers in a single analysis to assess the interest of a combined approach. First, we applied Single Nucleotide Polymorphisms to assess population structure at an evolutionary scale. Then, we tested for spatial segregation of the subpopulations using otolith shape as an integrative tracer of life history. Finally, we combined the genotypes and otolith phenotypes in a supervised machine learning framework to probabilistically assign adults to subpopulations. Genetic assignments and otolith shape analyses provided congruent results suggestive of a metapopulation structure for the common sole of the Eastern English Channel. Despite congruent results from genetics and otolith shape, the combined analysis did not provide realistic reallocation probabilities. Our findings support the idea that independent analyses of tracers provide fruitful insights and that a combined approach should be preferred when a large and balanced number of fish is available for each tracer analyzed.