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A compact, low cost and portable microelectrophoresis as a diagnostic tool is developed to investigate the surface charge study. An inverted lens webcam is employed to interface the images of charged particles to the computer. Mobility of charged particles was then being able to calculate. Meanwhile, special trays were designed to hold the samples which suspending in liquid phases. These designs included rectangular and square trays. Comparison between the designs of the trays for surface charge investigation was essential for further study on other charged particles. In this paper, the detail of setting for microelectrophoresis system was discussed and samples such as pollen were used to study its surface charge to verify the feasibility of the device. The study was focused on a range of voltages supplied to the pollen, namely Bougainvillea glabra to study the effects on its surface charge. The modified webcam was successfully to determine the EPM of the Bougainvillea glabra. The shape of the pollen can be shown clearly under the modified webcam as well. In conclusion. the modified webcam is a workable device for the surface charge testing.