A homogeneous fluorescence polarization immunoassay (FPIA) based on a monoclonal antibody was successfully developed and applied in the determination of clothianidin in agricultural samples. Three fluorescein-labeled clothianidin tracers containing different bridge lengths (2-, 4-and 6-carbon bridges) were synthesized and employed to investigate the effect of tracer structures on the FPIA. Under optimal conditions, the fluoresceinthiocarbamyl hexamethylenediamine-labeled clothianidin conjugate (HMDFlabeled clothianidin), which contains a 6-carbon bridge, performed most sensitively in the FPIA for detecting clothianidin, and the detection was achieved by one step in 12 min with a limit of detection of 5.53 ng mL À1 and an IC 50 of 0.0873 mg mL À1 . There were no obvious cross-reactivities of the antibodies with the analogues except for dinotefuran. Recoveries, measured in spiked water, soil, rice, apple, and cabbage samples, ranged from 78.7% to 108.2% with relative standard deviations less than 12.9%. Furthermore, the FPIA for authentic samples showed reliability and high correlations with ELISA of 0.9845 and HPLC of 0.9653. The developed FPIA demonstrated high sensitivity and accuracy, and could be ideally suitable for rapid, simple, and high-throughput screening for clothianidin contamination in agricultural samples.