Compost biobeds can promote biodegradation of pesticides. The microbial community structure changes during the composting process, and simple methods can potentially be used to follow these changes. In this study the microbial identification (MIDI) and ester-linked (EL) procedures were used to determine the composition of fatty acid methyl esters (FAMEs) in composts aged 3 and 12 months, inoculated with 3 recalcitrant pesticides (azoxystrobin, chlorotoluron, and epoxyconazole and a coapplication of all three) after 0, 56, and 125 days of degradation. Pesticide persistence was high, and after 125 days the residue was 22 to 70% of the applied amount depending mostly on the composting age. Seventy-one FAMEs belonging to nine groups were detected. The EL method provided three times as many detections as did the MIDI method and was more sensitive for all FAME groups except alcohol. Thirty-six and five FAMEs were unique to the EL and MIDI methods, respectively. The extraction method was of importance. The EL method provided a higher number of detections for 57 FAMEs, and the MIDI method provided a higher number for 9 FAMEs, while the two methods were equal for 5 FAMEs; thus, the EL method provided a more uniform overall FAME profile. Effects of the other factors were not always clear. Inoculation with pesticide did not influence the FAME profile with the MIDI method, while it influenced cyclopropane and monounsaturated content with the EL method. Composting age and degradation time had an effect on some groups of FAMEs, and this effect was greater with the EL method. The use of some FAMEs as biomarkers to follow microbial community succession was likely influenced by the type of compost and other factors.Plant protection has become a key factor in intensive agriculture, but the widespread use of pesticides can be toxic to nontarget organisms and can lead to ecosystem alterations. Formulated chlorotoluron (a herbicide), azoxystrobin (a fungicide), and epoxyconazole (a fungicide) are commonly used at the postemergence stage mainly for cereals, to control broadleaved weeds and grasses and to control some foliar and soilborne diseases, respectively.Most information on pesticide persistence is derived from registration documents, few studies appear in the scientific literature, and independent research is always suggested. A recent pesticide database (Footprint, 2007; http://www.eu -footprint.org/ppdb.html, accessed April 2010) reports half-life values (days) in soil, derived from laboratory studies at 20°C, of 73.5 for azoxystrobin, 59 for chlorotoluron, and 226 for epoxyconazole. However, a certain variability exists, and in other research half-lives are longer, i.e., more than 2 years (at 10°C) for epoxyconazole (4), 62 to 107 days for azoxystrobin (10), and 30 to 200 days for chlorotoluron (36), showing that significant degradation should be measured on a time scale of months or years (8, 9) according to the results of a recent review on pesticide persistence (3).The use of such persistent pesticides on agricultural fi...