The common selenium oxoanions selenite (SeO3(2-)) and selenate (SeO4(2-)) are toxic at intake levels slightly below 1 mg day(-1). These anions are currently monitored by a variety of traditional analytical techniques that are time-consuming, expensive, require large sample volumes, and/or lack portability. To address the need for a fast and inexpensive analysis of selenium oxoanions, we present the first microchip capillary zone electrophoresis (MCE) separation targeting these species in the presence of chloride, sulfate, nitrate, nitrite, chlorate, sulfamate, methanesulfonate, and fluoride, which can be simultaneously monitored. The chemistry was designed to give high selectivity in nonideal matrices. Interference from common weak acids is avoided by operating near pH 4. Separation resolution from chloride was enhanced to improve tolerance of high-salinity matrices. As a result, selenate can be quantified in the presence of up to 1.5 mM NaCl, and selenite analysis is even more robust against chloride. Using contact conductivity detection, detection limits for samples with conductivity equal to the background electrolyte are 53 nM (4.2 ppb Se) and 380 nM (30 ppb) for selenate and selenite, respectively. Analysis time, including injection, is ∼2 min. The MCE method was validated against ion chromatography (IC) using spiked samples of dilute BBL broth and slightly outperformed the IC in accuracy while requiring <10% of the analysis time. The applicability of the technique to real samples was shown by monitoring the consumption of selenite by bacteria incubated in LB broth.