Habitat fragmentation tends to cause isolation between populations of species that depends of that particular habitat. However the existence of microhabitats into the matrix could endure this fragmentation process. Thus we aim to test how habitat fragmentation resulting from processes of use and modification of the landscape, reduce the availability of suitable microhabitats for certain species and therefore restricts population connectivity. Thus, the understanding of how matrices and microhabitats acts in the functional and structural connectivity, could lead us to propose future management policies with the aim to maintain migration and dispersion rates between (sub) populations. For this, we will used the clay robber frog (Haddadus binotatus), because its’ sensitivity to habitat modification processes and its characteristic as excellent environmental indicator of one of the most degraded biomes in Brazil, the Atlantic Rainforest.