Soil biodiversity is the origin of considerable goods for maintenance and extension of above ground biodiversity and environmental soundness. This study was carried out in Shirvan, Mashhad and Gonabad, three regions of Razavi and Northern Khorasan provinces, to determine soil characteristics and biodiversity in natural systems of arid and semi-arid regions. In each studied system, 10 locations were selected for sampling and 50 soil samples were taken from each system with 0.3m length, 0.3m width and 0.3m depth.Texture, pH, organic matter, diversity and abundance of soil invertebrates, nematodes, bacteria, protozoa and mycorrhiza were measured in soil samples. Results showed with increasing of mean annual temperature and decreasing the mean annual precipitation, soil texture became coarser, pH increased and organic matter decreased from 0.38 to 0.05 percent. Soil invertebrates were found only in natural system of Shirvan, with low diversity and abundance. Abundance of soil nematodes and bacteria was similar in three regions. But diversity of soil bacteria, abundance of protozoa and diversity of mycorrhizal fungi reduced with increasing of mean annual precipitation and decreasing of mean annual temperature. Mean species richness of soil bacteria in natural systems of Shirvan, Mashhad and Gonabad was 5.3, 5.8 and 3.5, respectively. Species richness of mycorrhizal fungi in these systems was 5, 5 and 4 respectively. Based on results, climate and edaphic conditions were caused to restriction of biodiversity in arid regions. But conservation of this level of soil biodiversity and its goods has the special importance.