Soil aggregation is a dynamic process in which plants and the soil microbiota play a major role. This experiment was conducted to determine whether the effects of mycorrhizae on the stability of water-stable soil aggregates (WSA) and on selected groups of soil microorganisms are interrelated. Soil containers consisting of four compartments were utilized. Two compartments on each side of a solid barrier were separated by a 43 μm screen that permitted the passage of hyphae, but not of roots. The roots of Sorghum bicolor plants were split over the center barrier, and the roots on one side were inoculated with an arbuscular-mycorrhizal (AM) fungus. This design produced mycorrhizosphere soils (M) by AM roots or hyphosphere (H) soils by AM hyphae in the two compartments on the one side of the barrier, and rhizosphere soils (R) by nonAM roots or root- and hypha-free bulk soil (S) in the two compartments on the other side. At harvest (10 wk), there were significant differences in WSA between soils in the order: M>R>H>S, and WSA stability was significantly correlated with root or hyphal length. Numbers of colony-forming units of the microflora (total bacteria, actinomycetes, anaerobes, P solubilizers, and nonAM fungi) were in general not correlated with root or hyphal length, but in some cases were significantly correlated with WSA. Bacteria isolated from the water-stable soil-aggregate fraction tended to be more numerous than from the unstable fraction. The difference was significant in the M soil for total bacteria and P solubilizing bacteria. NonAM fungi were more numerous in the unstable fraction of the M soil. The data show that the root and fungal components of mycorrhizae enhance WSA stability individually and additively in concert, and suggest that they affect microorganism numbers indirectly by providing a favorable and protective habitat through the creation of habitable pore space in the WSA.