Greater productivity under intercropping has been attributed to the complementary use of environmental resources. However, the rooting pattern of component species under intercropping, which is an important morphological feature considering the complementary uptake of nutrients, has been studied only rarely under field conditions because of inherent technical difficulties. We examined rooting patterns of three green manure species, both sole cropped and intercropped, using a newly developed multi-color staining technique. Species were chosen from different functional groups: sorghum (Sorghum bicolor (L.) Moench.), a C4 grass; crotalaria (Crotalaria juncea L.), a legume; and sunflower (Helianthus annuus L.), a C3 dicot. We also investigated these species' aboveground biomass and N uptake. Sorghum distributed roots deeper under intercropping than under sole cropping; it was the most important contributor to increased biomass under intercropping. Crotalaria had a deep rooting system under both sole cropping and intercropping. Sunflower, with a shallow rooting system, was suppressed extremely under intercropping, possibly because of water deficiency in late in the season. The rooting patterns of green manure species examined using multi-color staining were related closely to the aboveground performance of these species under intercropping.