To understand the mechanism responsible for the enhanced accumulation of soil organic matter (SOM) under long-term use as a rice paddy, soil samples from the plow layer from 16 fields that have been used for irrigated rice production from 5 to 2000 years in the Hangzhou Bay, China, were analyzed. The humin in silt/clay particles was isolated as a representative relatively stable SOM pool, and isotopic signatures (δ 13 C, δ 15 N, and 14 C concentration), 13 C nuclear magnetic resonance (NMR) spectra, and biodegradability in an incubation were examined. The amounts of C and N in the bulk soil, silt/clay, and silt/clay-humin increased with increasing period of use as a rice paddy within the east and west zones, respectively. The degree of humification determined for humic acids indicated that the progression of humification did not contribute to the accumulation of C beyond 100 years. The δ 15 N of silt/clay-humin suggested an increase in organic N derived from chemical fertilizer or recent biological fixation with increasing amount of this fraction. The 14 C concentration showed a negative correlation with the amount of silt/clay-humin C. The structural property with regard to 13 C NMR spectra and biodegradability of the silt/clay-humin remained constant with the length of use as a rice paddy or 14 C concentration. These results suggest that the larger C or N accumulation in the soils with a longer rice paddy history can be attributed to an enhancement in the accumulation of recently generated SOM rather than the stable accumulation of humus over the years.