Arbuscular mycorrhizal fungi (AMF) are obligate biotrophs, known to play an important role in ecological processes. Conventional light microscopy is the most common method used to detect their presence in planta, but this method fails to discern the presence of multiple AMF species and is not quantitative. These two factors are critically important in ecological studies, where the symbiotic contribution of each isolate needs to be defined. This paper describes the use of quantitative real-time PCR (qRT-PCR) as a detection system to address this issue. We used two Glomus spp., namely, G. intraradices and G. mosseae, to show that it is possible to study the interactions between these two isolates during the cocolonization of a single root system. Three different physiological studies were set up to assess how the interactions affected the occupancy of these fungi intraradically on a temporal basis. These treatments included saline and phosphorus stress, spatial distribution in the root zone, and preference for a particular host. qRT-PCR could prove a valuable tool in the area of AMF field ecology, where such data are critically important for defining the role of each species in the community structure.