Abstract: Fatty acids as major compounds of soil lipids may affect many soil properties, but the input and turnover rates in soil are largely unknown. The objective of this study was to identify and quantify fatty acids in soils as a result of input from primary sources such as plant residues, farmyard manure and soil organisms, and to evaluate the corresponding turnover- and stabilization processes. The concentrations of n-C10:0 to n-C34:0 fatty acids were determined in the Ap horizon of a Phaeozem with long-term cropping of rye and maize and the treatments ‘Unfertilized’ (‘U’) and fertilized with ‘Farmyard manure’ (‘FYM’). The most important primary sources of fatty acids such as rye and maize stubble and roots, soil micro- and mesofauna, and the applied FYM were also investigated. The quantification of fatty acids by gas chromatography/mass spectrometry (GC/MS) showed that long-term FYM application led to larger concentrations of n-alkyl fatty acids in the plots grown with rye (‘U’: 48.1μgg−1, ‘FYM’: 57.7μgg−1, **P≤0.01, n=3) and maize (‘U’: 17.0μgg−1, ‘FYM’: 23.4μgg−1, ***P≤0.001, n=3). The observed bimodal fatty acid distribution in soils from n-C10:0 to n-C21:0 and from n-C21:0 to n-C34:0 with a predominance at n-C16:0 and at n-C28:0 was apparently due to input from crop residues, soil organisms and FYM. The short-chain lengths may have originated from the investigated primary sources. The major contributors to the long-chain lengths, with a maximum at n-C28:0, were rye stubble and FYM. A change in mono-culture from rye to maize, 38 years prior to sampling, led to a decrease in fatty acid concentrations by factors of about 2.8 (‘U’) and 2.5 (‘FYM’). Therefore, rye-derived fatty acids and soil tillage had a larger impact on fatty acid pools than the input of primary organic matter. The changes in fatty acid distributions and pools under the consideration of the quantified input of primary organic matter led to the conclusion that the short-chained fatty acids were more rapidly decomposed than the long-chains. [Copyright &y& Elsevier]