The species of Cr(III) and Cr(VI) in water samples were determined by flow injection on-line preconcentration and separation on two-microcolumn system-derivative flame atomic absorption spectrometry during a collaborative analysis for certification. The Cr(III) and Cr(VI) in water samples were retained on two microcolumns with ion exchange resin and were eluted directly to nebulizer by 15% HNO3 and 8% NH4NO3, respectively. The characteristic concentration (at the sensitivity grade of 2 mV min-1 for 1 min of preconcentration time) for Cr(III) and Cr(VI) were 0.130 and 0.0985 μg l-1, in the order which were 332- and 431-fold better than those of FAAS, and 45- and 47-fold better than those of FI-FAAS, respectively. The relative standard deviations were 3.27% and 3.66% with corresponding detection limits (3σ) of 0.244 and 0.235 μg l-1, respectively. The linear ranges of determinations for Cr(III) and Cr(VI) were 0~100 μgm l-1 with correlation coefficients of 0.9984 to 0.9996. The satisfactory recovery of 94.4%~106% for Cr(III) and Cr(VI) could be obtained from water samples.