The external hypha of arbuscular mycorrhizal (AM) fungi, extending from roots out into soil, is an important structure in the uptake of phosphate from the depletion zone around each root. In this paper, we analysed some phospholipid fatty acids (PLFAs) derived from external hyphae of four AM fungi (Glomus etunicatum, Glomus clarum, Gigaspora margarita and Gigaspora rosea) to find fatty acids which may be useful as specific markers for identifying and quantify the external hyphae of Gigaspora species. Leek (Allium porrum L.) seedlings inoculated with each AM fungus were grown in river sand. Sand samples were collected and four PLFAs (16:1omega5, 18:1omega9, 20:1omega9 and 20:4) in the sand were analysed. In addition, the hyphal biomass in the sand was determined by the direct microscopic method. PLFAs 18:1omega9 and 20:4 were found in all the AM-inoculated and non-inoculated sand samples. PLFA 16:1omega5 was detected in the sand inoculated with G. etunicatum, G. clarum and Gi. rosea. PLFA 20:1omega9 was detected only in the sand inoculated with Gi. rosea. PLFAs 16:1omega5 and 20:1omega9 were not found in the sand inoculated with Gi. margarita. The amount of PLFA 20:1omega9 was closely correlated with the amount of biomass of external hyphae of Gi. rosea (r = 0.937, P < 0.001), whereas no correlation was observed for PLFA 16:1omega5. The 20:1omega9 content of Gi. rosea was approximately 6.56 nmol mg(-1) hyphal biomass. We suggest that PLFA 20:1omega9 can be used as a specific marker for identifying and quantifying the external hyphae of Gi. rosea, at least in controlled experimental systems. (C) 2004 Elsevier Ltd. All rights reserved.