The objective of this study was to examine the effects of long-term (18 years) fertilization on contents and distributions of amino sugars within aggregate-size fractions of a clay soil (Udolls, USDA Soil Taxonomy System). Treatments included unfertilized control (CK), mineralization fertilization (NP), and application of mineral fertilizers plus pig manure (NPM). Soil samples were collected from the 0-20-cm layer and fractionated to aggregates of different sizes (> 2,000 mu m, 250-2,000 mu m, 53-250 mu m, and < 53 mu m) by wet sieving. Glucosamine (GluN) and muramic acid (MurA) were used as biomarkers for fungal and bacterial residues, respectively. Results showed that NPM significantly increased the concentrations of total amino sugars in all aggregate-size fractions compared with the CK treatment. This occurred concurrently with an increase in mean weight diameter of water-stable aggregates and soil organic C content. Higher concentrations of total amino sugars in macroaggregates (> 250 mu m) of NPM soils were mainly due to a relatively greater accumulation of GluN over MurA, which suggests that accumulation of fungal residues is important for soil aggregation and organic C storage in the tested soil. By contrast, mineral fertilization was ineffective on soil aggregation and amino sugar accumulation. Furthermore, GluN was relatively enriched in fractions of > 250 mu m while MurA was generally enriched in the 53-250-mu m fraction. This indicates that there are specific mechanisms of fungal and bacterial enrichment in different aggregate-size fractions.