Typically anadromous, the twaite shad (Alosa fallax) can become landlocked and adapt to a fully freshwater life. The only landlocked shad population in Northwestern Europe is found in a lake in Ireland, Lough Leane. The Killarney shad, Alosa killarnensis (or Alosa fallax killarnensis, as it is mostly referred to) displays a level of morphological divergence that indicates a long-term isolation in the lake. Microsatellites and mtDNA control region sequences were used within a coalescent framework (BEAST and Approximate Bayesian Computation (ABC)) to investigate its colonization history and to clarify its taxonomic status. Results indicate that the lake was likely colonised in two independent events, the first coinciding with the retreat of the ice sheet from the area after the Last Glacial Maximum and the second after the Younger Dryas. Microsatellite data has shown that these two landlocked lineages have completely admixed within the lake, and have started diverging significantly from their closest ancestor, the twaite shad. We argue that our molecular results (together with the life-history and physiological divergence between Killarney and twaite shad) are conspicuous enough to view the landlocked population as a new species, and one whose future existence would certainly not be insured by its sister taxon.