Inundation of paddy soils for submerged rice production strongly impacts soil formation. Here we used chronosequences with up to 2000 years of cultivation history to compare soil formation in non-inundated (non-paddy) cropping systems with the formation of soils used for paddy rice production. This approach allowed us to identify the influence of agricultural management at different stages of pedogenesis. Soil samples were taken from two chronosequences derived from uniform parent material in the coastal region of the Zhejiang Province (P.R. China). One chronosequence consisted of paddy soils of different ages (50-2000 years), characterized by a yearly cropping sequence of rice cultivation under flooded conditions alternated with a non-inundated crop. The adjacent non-inundated (non-paddy) chronosequence was exclusively used for non-inundated crop production for 50-700 years. Lipid biomarkers revealed origin and homogeneity of the original coastal sediments and enabled the reconstruction of a consistent land use history for both chronosequences. The chronological development of soil properties and horizons suggested that the formation of paddy soils can be subdivided into three phases. The initial phase of paddy soil development takes only a few decades and is dominated by desalinization and formation of a compacted plow pan, leading from Fluvisols to Anthraquic Cambisols. During the next centuries (second phase), the differentiation between paddy and non-paddy management becomes increasingly obvious in terms of accelerated carbonate losses and constantly increasing organic carbon concentrations in paddy topsoils. In the third stage of paddy soil development (≥ 700 years), a (trans-)formation and redistribution of oxides is accompanied by clearly visible hydromorphic patterns in paddy subsoils, thus promoting further development from Cambisols to Hydragric Anthrosols. To account for the underlying processes we suggest modifying the depth and mottling criteria for the definitions of anthraquic and hydragric soil horizons in the classification of the World Reference Base for Soil Resources. The non-paddy chronosequence was characterized by a low degree of soil development in which decalcification-related processes dominated throughout 700 years of soil formation. Hence, soil formation under paddy management was accelerated relative to that under dryland cropping, even though the 2000-year-old paddy soils lacked evidence of an advanced stage of silicate weathering, formation of pedogenic clay minerals, or clay migration.