Cyanobacteria are widespread photosynthetic microorganisms among which some are able to fix atmospheric nitrogen. We investigated the impact of indigenous cyanobacteria strains (Nostoc) inoculation on physical characteristics of poorly aggregated soils from Guquka (Eastern Cape, South Africa). The soil aggregates (3–5 mm) were arranged into a layer of 10–20 mm thick, and sprayed with cyanobacteria solution. Subsequently the inoculated and un-inoculated samples were incubated (30C, 80% humidity, continuous illumination at 100 lmol m–2 s–1). Their micromorphological characteristics and aggregate stability were investigated, after 1, 2, 3, 4 and 6 weeks of incubation, by using high resolution Cryo-SEM and aggregate breakdown tests.Micromorphological investigations revealed that the surface of uninoculated samples remained uncovered, while the inoculated samples were partially covered by cyanobacteria material after one week of incubation. Adense superficial network of cyanobacterial filaments and extracellular polymer secretions (EPS) covered their surface after 4 and 6 weeks of incubation. Organo-mineral aggregates comprising cyanobacterial filaments and EPS were observed after 6 weeks of incubation. The results of aggregate breakdown tests showed no significant difference between un-inoculated samples after 1, 2, 3, 4 or 6 weeks, while they revealed improvement of aggregate stability for inoculated samples. The improvement of aggregate stability appeared in a short while following inoculation and increased gradually with time and cyanobacteria growth. The increase in aggregate stability is likely related to the changes induced in micromorphological characteristics by cyanobacterial filaments and EPS. It reflects the effect of coating, enmeshment, binding and gluing of aggregates and isolated mineral particles by cyanobacteria material.