To study the impact of long-term application of organic amendments and fertilizer nitrogen on C sequestration and its distribution among various physical pools of soil organic matter in rice-wheat system. We studied the distribution of organic C among physical pools of soil organic matter separated by size and density floatation techniques in a sandy loam soil after 11 years of rice-wheat cropping with continuous application of farmyard manure (FYM), rice straw (RS), and fertilizer nitrogen (N). Laboratory incubation experiments were conducted to estimate mineralizable C in soil and relate it to various organic C pools. Application of FYM and RS increased soil organic carbon (SOC) stocks in the surface soil by 33.7 % over sole application of fertilizer N. Conjoint use of FYM and RS along with fertilizer N caused the greatest (83.5 %) increase in SOC stocks. Particulate organic C (POC) constituted 23-34 % of SOC with 2.8 to 11.3 % as coarse POC (cPOC) and 17.5-22.6 % as fine POC (fPOC). The cPOC responded to management to a greater extent than fPOC and may thus be considered a more labile pool of SOC. The coarse particulate organic matter (cPOM) had wider C/N ratio (11.1 to 12.7) than the fine POM (fPOM; 8.2 to 9.9). Mineral associated organic C (MinOC) represented the greatest proportion (48-68 %) of SOC followed by heavy fraction (HFOC; 21-30 %) and light fraction organic C (LFOC; 5-15 %). Addition of FYM alone or in combination with RS enlarged the LFOC pool by 263 and 383 %, and HFOC pool by 62 and 127 %, respectively with insignificant effect on MinOC. Rice straw increased LFOC by 66 %, with no effect on HFOC. The C/N ratios generally decreased as the soil organic matter (SOM) fractions became finer and followed the order LFOM > iLFOM > HFOM > MinOM. Mineralizable C in the surface soil was significantly related to SOC (R (2) = 0.90), LFOC (R (2) = 0.72) and HFOC (R (2) = 0.68). Application of organic amendments in rice-wheat system has a major influence on SOC and the relative distribution among various C pools. The LFOC is most sensitive to management, followed by sand-sized HFOC and silt- and clay-sized MinOC pool suggesting thereby that these may be considered to represent active, slow and passive pools of SOC, respectively. The conjoint use of FYM, RS and fertilizer N could maintain SOC almost at the same level as for the uncultivated soil and this practice may help in maintaining the sustainability of rice-wheat cropping systems in the Indo-Gangetic plains.