Electroencephalography (EEG) is a standard tool for monitoring brain states in humans. Understanding the molecular and cellular mechanisms underlying diverse EEG rhythms can be facilitated by using mouse models under molecular, pharmacological, or electrophysiological manipulations. The small size of the mouse brain, however, poses a severe limitation in the spatial information of EEG. To overcome this limitation, we devised a polyimide based microelectrode array (PBM array) with nanofabrication technologies. The microelectrode contains 32 electrodes, weighs 150 mg, and yields noise-insensitive signals when applied on the mouse skull. The high-density microelectrode allowed both global and focused mapping of high resolution EEG (HR-EEG) in the mouse brain. Mapping and dynamical analysis tools also have been developed to visualize the dynamical changes of spatially resolved mouse EEG. We demonstrated the validity and utility of mouse EEG in localization of the seizure onset in absence seizure model and phase dynamics of abnormal theta rhythm in transgenic mice. Dynamic tracking of the EEG map in genetically modified mice under freely moving conditions should allow study of the molecular and cellular mechanisms underlying the generation and dynamics of diverse EEG rhythms.