The long term effect of crop residue and residual zinc on Zn fractions in soil and their contribution to Zn uptake in rice-wheat system was studied in calciorthents of the Rajendra Agricultural University, Pusa, Samastipur (Bihar) during 2010–11 and 2011–12. Application of zinc and crop residue increased the water soluble+exchangeable, complexed, organically bound, carbonate and amorphous oxide, crystalline oxide, residual and total Zn in the soil. The order of dominance of different fractions in soil was total Zn (164.35 mg/kg)> residual-Zn (156.41 mg/kg) >Zn bound to crystalline oxide (3.06 mg/kg)>complexed Zn (2.27 mg/kg)>organically bound Zn (1.14 mg/kg)> water soluble plus exchangeable Zn (0.84 mg/kg) and Zn bound carbonate and amorphous oxide (0.73 mg/kg). All the soil Zn fractions were significantly correlated among themselves indicating existence of a dynamic equilibrium with each other. Zinc uptake by rice-wheat was improved with zinc along with crop residue plus compost. Among different Zn fractions, Zn bound to crystalline oxide, followed by Zn bound to carbonate and amorphous oxide played a key role in explaining the variation in yield and nutrient uptake by rice and wheat. The highest zinc uptake by rice and wheat was reported with the conjoint use of 100% crop residue and 10 kg Zn/ha.