The paper is concerned with the Nitsche mortaring in the framework of domain decomposition where non-matching meshes and weak continuity of the finite element approximation at the interface are admitted. The approach is applied to singularly perturbed reaction-diffusion problems in 2D. Non-matching meshes of triangles being anisotropic in the boundary layers are applied. Some properties as well as error estimates of the Nitsche mortar finite element schemes are proved. In particular, using a suitable degree of anisotropy of triangles in the boundary layers of a rectangle, we derive convergence rates as known for the conforming finite element method in presence of regular solutions. Numerical examples illustrate the approach and the results.