The fatty acid composition of pea roots with and without the root pathogen Aphanomyces euteiches was studied using whole cell fatty acids (WCFA), phospholipid fatty acids (PLFA) and neutral lipid fatty acids (NLFA). Initial screening for A. euteiches markers using WCFA analysis showed that the fatty acids 14[ratio ]1ω9, 14[ratio ]0, 20[ratio ]4 and 20[ratio ]5 were specific to roots infected with A. euteiches. The amounts of these fatty acids correlated positively with the percentage of the root system containing A. euteiches oospores, suggesting that they could be useful indicators of A. euteiches root-infection levels. Analysis of the composition of phospholipid fatty acids (PLFA) and neutral lipid fatty acids (NLFA) of pea roots with and without A. euteiches showed similar specificity as found with WCFA analysis. PLFAs and NLFAs specific to roots inoculated with A. euteiches were also present in mycelium from pure culture of A. euteiches. The PLFAs 14[ratio ]0, 20[ratio ]4 and 20[ratio ]5 were used to estimate biomass of A. euteiches and the NLFAs 14[ratio ]1ω9, 14[ratio ]0, 20[ratio ]4 and 20[ratio ]5 were used as indicators of energy reserves of the pathogen. The possible use of specific fatty acids to study growth and development of A. euteiches in pea roots is discussed.