The current technologies are utilizable for applying the electrophoresis through agarose or polyacrylamide gels. This standart method is used to seperate, identify and purify nucleic acids, and to get faster as well as more efficiently results by identifying the bands including the basepairs. In this study, Mini Gel Electrophoresis System Based Embedded System (MESBES) is developed to increase the sensibility and accuracy of electrophoresis system by using laboratory environment, and so this system achives to wipe-out the errors based on humans as well as laboratory environment. Additionally, this system also provides faster, more accure and easily accomplishment resulting of the analyses done in laboratory environments by the software of embedded system, microprocessor, human interface, remote access and software development features. MESBES has an upgradeable structure with the typical characteristics of embedded systems such as low power consumption, and updatable. During the process of electrophoresis, getting instantaneous data with user interface, taking band images by applying the UV to gel, at the end of the process transfering the band images to the electronic media automatically can be provided.