Arbuscular mycorrhizal fungi (AMF) may colonize several plant species simultaneously, thus receiving their carbon from different plants. In previous work, we have used microcosms with flax (a C3 plant) and sorghum (a C4 plant), connected to a common mycorrhizal network, in order to track the carbon source of AMF, making use of the distinct 13C/12C isotope compositions of C3 and C4 plants (Walder et al., 2012). Here we compare three methods for analysing the stable carbon isotope composition of AMF. Bulk carbon isotope analysis of washed extraradical mycelium is possible, but has the drawback of potential contamination from non-mycorrhizal sources. Bulk carbon isotope analysis of isolated AMF spores yields more reliable results but is rather tedious. We explain, in some detail, a more refined analysis based on the extraction of lipids from soil, followed by analysis of an AMF biomarker, the fatty acid C16:1u5.