This paper deals with the use of wavelets in the framework of the Mortar method.We first review in an abstract framework the theory of the mortar method fornon conforming domain decomposition, and point out some basic assumptionsunder which stability and convergence of such method can be proven. We studythe application of the mortar method in the biorthogonal wavelet framework.In particular we define suitable multiplier spaces for imposing weakcontinuity. Unlike in the classical mortar method, such multiplier spaces arenot a subset of the space of traces of interior functions, but rather oftheir duals.For the resulting method, we provide with an error estimate, which is optimal in thegeometrically conforming case.