The wealth of soil biodiversity is poorly known on both local and global scales, and thus the importance of soil organisms (microbes to invertebrates) has been largely disregarded in assessments of biodiversity consequences for ecosystem functioning. The huge abundance and numbers of species in soils as well as the diversity of methods required for sampling, extraction and identification of the organisms, have made assessments of diversity of all taxa at even one location extremely difficult. Despite that, we suggest that a better understanding of soil biodiversity and its relationship to critical ecosystem services is vital for planning for sustainable soils for the long term. A multitude of microbes, protozoa, invertebrates and vertebrates interact to maintain soil fertility, decay, recycling of organic matter, the breakdown of hazardous wastes, cleansing of water, the biological control of agricultural and human pests and the composition of the atmosphere. However, we have yet to identify which species play key roles in these processes, even those that may most directly and immediately further the human enterprise through influencing carbon sequestration, erosion control, the quality of food supply and biocontrol of pests. Much of the functioning in soil is carried out by communities of organisms and we need to know more about their structures. Urgency is added to this task because humans, through land use change and pollution, are impacting the biodiversity and functioning of soil organisms as well as that of organisms in interconnected habitats such as groundwaters, riparian and wetland systems, and aboveground habitats. The biotic groups and the ecosystem services we need to understand cross international boundaries and expertise on them is internationally distributed. International efforts are required to (a) synthesize available information on global soil biodiversity and functioning across ecosystems and (b) develop integrated research approaches and new technologies necessary to examine soil biocomplexity, if we are to acquire the information necessary to sustainably manage the soil as a primary natural resource.