The flow cytometry technique, based on the enumeration and multi -parametric analysis of suspended particles in a liquid medium, has enabled us to identify an population of viruses and bacteria in the soil and the digestive tract of earthworms. It appears that the p assage of the ground through the digestive tract of oligochaetes annelids would regulate bacterial and viral biomass of the soil as well as soil physico-chemical parameters. The soil microfauna is involved in the decomposition of the organic material and the nutrient bioavailability to plants and soil microorganisms. It also plays an important role in the creation and conservation of the soil structure. Apart fr om their role as "engineers", earthworms through their internal microfauna, participate in the regulation of physical and chemical parameters such as nitrogen mineralization. Earthworms thus participate in the processes of decomposition of organic material improve the bioavailability of minerals, maintain the porosity of the soil and increase the stability of the aggregates. Oligochaetes are expected to play a central role in the implementation of biological regulation in the agro-ecosystems essential to the development of ecological and intensive agriculture. Another reason to be interested in these soil organisms is that they are good candidates for bio-indicators. Indeed, the level of their population is sensitive to cultural practices, chemical products that are spread, quality and quantity of the resource in carbon, which are important characteristics of the sustainability of agricultural systems.