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Abstract The frequency dependence of electrokinetic particle trapping using large‐area (>mm²) conductive carbon nanofiber (CNF) mat electrodes is investigated. The fibers provide nanoscale geometric features for the generation of high electric field gradients, which is necessary for particle trapping via dielectrophoresis (DEP). A device was fabricated with an array of microfluidic wells for repeated experiments; each well included a CNF mat electrode opposing an aluminum electrode. Fluorescent microspheres (1 µm) were trapped at various electric field frequencies between 30 kHz and 1 MHz. Digital images of each well were analyzed to quantify particle trapping. DEP trapping by the CNF mats was greater at all tested frequencies than that of the control of no applied field, and the greatest trapping was observed at a frequency of 600 kHz, where electrothermal flow is more significantly weakened than DEP. Theoretical analysis and measured impedance spectra indicate that this result was due to a combination of the frequency dependence of DEP and capacitive behavior of the well‐based device.