Anatolia is a significant centre of biodiversity and endemism with diversity hotspots located mainly in mountain ranges. Its complex geological history and heterogeneous topography have generated natural barriers to gene flow that favour speciation, and migration corridors that accentuate its transitional biogeographic position. While more attention has been paid to the predominant Irano-Turanian and Mediterranean xerophytic elements, the evolution of species adapted to wet habitats with limited occurrence is understudied in this area. Here, we investigated Cardamine representatives in northern Anatolia with the aims of resolving the taxonomically uncertain populations previously assigned to either C. uliginosa or C. tenera from northwestern Anatolia (Uludağ,) and elucidating the genetic structure of (sub)alpine C. uliginosa recorded mainly from the North Anatolian Mts. (Pontic Mts.). Using a combination of phylogenomic (Hyb-Seq), morphometric, and flow cytometric analyses, we support a distinct position of the northwestern Anatolian populations, described here as a new species Cardamine anatolica. Apart from Uludağ, a few other sites were found in the montane to subalpine belts in the Marmara and Aegean regions. A sister phylogenetic position of C. anatolica to C. acris, a widespread and polymorphic Balkan species, supports the existence of biogeographic links between these areas and suggests a vicariance scenario. We revealed a pronounced intraspecific diversification of C. uliginosa with geographic structuring and admixture in the Pontic Mts., which highlights this area as a significant hotspot of biodiversity not only at the species level but also at the level of genetic variation. Due to the common misinterpretation of the species treated here, we revise their distributional data, provide details on their morphological differentiation, and present an identification key. The study highlights the evolutionary importance of Anatolian mountains, which promote speciation, favour accumulation of diversity, and serve as a meeting place of colonization routes.