The article describes the experience of landscape sites (geotopes) and elementary watersheds modeling with the ARCMAP tools for determination of valuable forests in poorly studied areas of the Russian Far East. The authors substantiate the possibility and expediency of simultaneous use of two different matrices which represents various properties of land cover – geostationary landscape sites matrix and geodynamic river basins matrix. Biodiversity is determined by the landscape heterogeneity. Landscape units – geotops – can be calculate/obtained via geomorphometry-and-landform tools in GIS software. Elementary river basin is functional unit of the landscape, providing its integrity with the transfer of matter and energy. Hydrological tools in GIS can implement the watershed modeling. Modeling involves a number of consecutive and interconnected operations. Choosing key factor of landscape differentiation via a tool «Landform Classification» for each geographic province. Primary geomorphology modeling – includes altitude levels, slope, aspect, plan and profile curvature, topographic index, height above the river, Euclidean distance to the river, flow direction, flow accumulation, stream raster. Secondary geomorphology modeling is a combination of primary rasters to obtain geotop network. Vegetation cover modeling consist of spatial imagery unsupervised classification for the generation of spectrally different vegetation classes. The final step – calculation of integrated (geotops and vegetation classes) diversity via Zonal statistic tool. The river basins with the highest potential level of biodiversity may be proposed for protection as one of the High Conservation Value Forests (HCVFs) categories.