The management of soil organic matter is crucial to the activities of soil biota. Use of green manures can have multi-faceted beneficial effects on crop productivity arising from increased biological activity and diversity of soil organisms, which in turn can lead to minimized damage and losses from soil borne pathogens, and increased activity of beneficial organisms. However, different sources of green manure can have different effects on the balance between populations of harmful and beneficial organisms. This is largely because green manures have different rates of decomposition, nutrient release and impact on soil moisture and temperature that invariably affects relative population sizes. We evaluated the effect of different types of green manure on three key functional groups of soil biota: 1) pathogens (root rots of beans), 2) microsymbionts (arbuscular mycorrhizal fungi-AMF) and 3) microregulators (nematodes). An experiment was established in 2003 at CIAT's Santander de Quilichao Research Station, using a plot that had a history of high incidence of bean root rot pathogens. The plots were planted with a susceptible bean variety A 70. Immediately after planting, plots were covered with three types of green manure: (1) rapidly decomposing Tithonia diversifolia (TTH), (2) intermediate rate of decomposition by Cratylia argentea; and (3) slow decomposing Calliandra calothyrsus (CAL) at a rate of 6 ton ha-1; and (4) the control (no green manure added). The experiment was replicated five times and samples were collected within and between rows, to measure the effect of the bean plant rhizosphere on soil biota studied. Following 6 cropping seasons, results revealed that application of Calliandra increased bean yield, reduced the incidence of root rots, increased AMF hyphal lengths and reduced nematode abundance. For treatments receiving Cratylia, minor differences were observed for root rot incidence, yield and nematode abundance, but AMF hyphal lengths were increased when compared to control. Although showing greater AMF hyphal lengths and lower disease incidence, bean yields in plots receiving Tithonia were lower than that obtained in control plots. These results highlight the complexity of interactions among soil biota and impacts on crop yields. The potential exists that green manures promote unknown beneficial organisms that can potentially be used to manage root rot pathogens and/or promote plant growth. The full extent of the impact of this study will be realized upon completion of studies to characterize the abundance and functional diversity of microorganisms from this long-term experiment.