Organochlorine pesticides have been extensively used for many years to prevent insect diseases of rice (Oryza sativa L.), but little is known about their residual impacts on the underground micro-ecology in anaerobic environment. In this glasshouse study, we characterized the lindane effects on the assembly of root-associated microbiomes of commonly used indica, japonica and hybrid rice cultivars, and their feedback in turn, in modifying lindane anaerobic dissipation during 60 days' rice production. The results showed that rice growth inhibited the anaerobic dissipation of lindane, but was not affected apparently by lindane at initial spiked concentration of 4.62 and 18.54 mg kg-1 soil. Suppressed removal of lindane in rice planted treatments as compared with that in unplanted control was likely due to inhibited reductive dechlorination induced by a comprehensive effect of radial O2 secretion of rice root and co-occurring Fe(III) reduction that consumed electron competitively in rice rhizosphere. However, the hybrid cultivar exhibited a less suppression than the conventional cultivars in high polluted soils. Bacteria was more sensitively responded to lindane pollution than fungal taxa, and Actinobacteria, Chloroflexi, Verrucomicrobia and Proteobacteria were the main different phyla between hybrid and conventional cultivars, with a more stable community structure exhibited in the hybrid rice under lindane stress. Our study highlights the assembly and variation of root-associated microbiomes in responses of lindane pollution, and suggests that hybrid rice cultivar might be most competent for cultivation in paddy fields polluted by lindane and other organochlorine pesticides, especially in the area with high residual levels.