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Long-term soil chronosequences are valuable model systems for investigating pedogenesis and investigating the process of element coupling. Here, we assessed the coupling relationships among C, Fe, and Fe-reducing bacteria (Anaeromyxobacter, Geobacter, and Shewanella) in a paddy soil chronosequence of approximately 50 to 1000 years. Soils of the chronosequence originated from tidal marsh under nearly identical landscape and climate conditions. During 1000 years of rice cultivation, soil organic carbon (SOC) contents in surface horizons (0–20 cm) increased from 10.4 to 21.8 g kg−1. In contrast, total Fe contents declined from 59.6 to 45.1 g kg−1 during the initial 50 years of paddy rice cultivation and then further decreased at a low rate of 0.004 g kg−1 soil year−1 (equivalent to 10 kg ha−1 soil year−1). Organically complexed Fe oxides (Fep) increased from 219 to 642 mg g−1 with increasing time of pedogenesis, but free total Fe oxides (Fed) and amorphous Fe oxides (Feo) declined at early stage of soil development, followed by a slow accumulation at later stages of the chronosequence. Gene copy numbers of Anaeromyxobacter and Geobacter increased from 4.6 × 105 and 3.6 × 106 copies g−1 to 3.8 × 107 and 3.6 × 107 copies g−1 dry soil with continuous paddy rice cultivation, while concurrently Shewanella gene abundance decreased gradually from 4.5 × 105 to 9.3 × 104 copies g−1 dry soil. Using structural equation modeling (SEM), different coupling relationships were observed among C, Fe, and Fe-reducing bacteria for the first 300 years of paddy chronosequence and thereafter. Overall, all Fe-reducing bacteria did not show consistent variation. With the stable microbial community and iron oxide fractions, the microbially mediated dissimilatory coupling relationship between C and Fe becomes simple during 1000 years of paddy soil development. [ABSTRACT FROM AUTHOR]