Aggregates derived from senescent phytoplankton populations and associated microbial assemblages were incubated aerobically in the dark to assess the compositional changes in lipids during the degradation of artificial marine snow. The prevalence of saturated over unsaturated fatty acids indicated that aggregates were already degraded when incubation started. Nonetheless, the lipids in the artificial aggregates were quickly further degraded as indicated by a depletion in short-chain (b20) saturated and monounsaturated fatty acids. In contrast, the concentrations of long-chain (N20) saturated fatty acids fluctuated, suggesting that some of these lipids could have been produced in situ by marine microorganisms rather than deriving from higher plant debris. In addition, a bacterial branched monounsaturated fatty acid (11-methyloctadecenoic acid), which has not been found previously in marine particles was present in artificial aggregates. Molecular (16S rRNA gene) analyses indicate that the bacterial community attached to aggregates is dominated by (predominantly uncultured) ฮฑ-Proteobacteria, ฮณ-Proteobacteria and Planctomycetes. Of these, a Roseobacter sp. which was present in artificial aggregates analysed in a parallel study (Balzano et al. 2009, Aquatic Microbial Ecology 54:291-303), can contain 11-methyloctadecenoic acid, and other bacteria present in artificial aggregates have the potential to produce long-chain saturated fatty acids. Thus, the fatty acid assemblage appears to reflect both organic matter degradation, including selective preservation, but also changes in the microbial assemblage.