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Phospholipid fatty acids (PLFAs) were analysed at different time periods during composting of two waste mixtures rich in fats, M1 (22%) and M2 (39%), with the aim of monitoring changes in microbial community structure. The two mixtures consisted of a sludge sample collected from a vegetable oil refinery effluent treatment plant combined with household wastes. The PLFA profiles of both mixtures revealed that, at the start of the process, fungi and Gram-negative bacteria (GÀ) were more abundant in M2 than in M1. During the thermophilic phase, branched PLFA (i15:0, a15:0, i16:0, and i17:0) markers of Gram-positive bacteria (Gþ), became more abundant in M1, while G-bacteria were predominant in M2. The PLFA profiles in M1 representing non-specific, Gþ and GÀ bacteria as well as fungi decreased during the cooling phase (maturation) while an increase was recorded in M2, which was richer in fats. The ShannoneWeaver diversity index (Ish) showed a greater increase during M1 composting (from 0.69 to 1.05), mainly for Gþ bacteria and GÀ bacteria, than in M2 composting (from 0.79 to 0.84). Principal components and cluster analyses revealed a succession of different communities during composting, which varied from fungi and GÀ bacteria to Gþ and thermophilic and thermotolerant GÀ bacteria. The end of composting was characterized by a reduction of all these microbial entities, especially for M1, except actinomycetes, which are associated with compost stability.