The work offers the system of the estimates to range territorial complexes by density of biological diversity and to allocate potential refugia of a biota. This is relevant in the conditions of high degree of alteration of flat Adyghea. The GIS analysis of data of space monitoring and results of inventory of distribution of 179 protected species gives grounds to select nine potential refugia – microclusters of a natural ecological framework. Research is made to develop approaches to projection of missing links of a natural framework in the conditions of high degree of territory alteration.