The obligately symbiotic nature of glomalean endomycorrhizal fungi poses unique problems for studying the systematics of the group. Because of the interdependence of these fungal symbionts and plants, the stability of potential taxonomic characters must be evaluated prior to their use in comparative studies. In this study, the efficacy of fatty acid methyl ester (FAME) profiles as taxonomic tool was assessed by comparing profiles of up to four successive 'generations' of pot cultures of eight isolates representing all families in Glomales. Since pot-cultured material of ancestral generations was stored at 4 degrees C, stability of FAME profiles with prolonged storage also was tested. The stability of FAME profiles of fungi subjected to different symbiotic conditions was tested by growing five glomalean isolates on three host plant species (Asparagus officinalis, Sorghum bicolor and Trifolium pratense). Unweighted numerical analysis revealed that FAME profiles of all isolates tested were similar among the various pot culture generations and after storage up to 22 months. The profiles of fungal isolates grown on the different plant species also were similar, suggesting that host physiology was not a significant factor in causing modifications to composition or abundance of fatty acids. The stability and heritability of FAME profiles are now justified for use in comparative studies at the species level and above for taxonomic, and possibly systematic, investigations.