The aim of this study was to investigate the changes of the association between cardiac activity and the electromyographic (EMG) level of the antagonistic jaw muscles during chewing and NREM sleep in guinea pigs after systemic clonidine injections. Ten animals were prepared for chronic experiments to monitor sleep, cardiac activity and EMG activity of jaw-closing masseter (MAS) and jaw-opening anterior belly of digastric (ADG) muscles. The recordings were made for ten hours with the injections of saline or clonidine (10μg/kg, i.p.). Integrated EMG activity of the two muscles and mean heart rate (mHR) were calculated for every 10-s epoch. During the two hours after clonidine injection, the duration of REM sleep and mHR were significantly reduced. During chewing, the high EMG activity level of the two muscles and the activity ratio between the two muscles were not modified although mHR was decreased. During NREM sleep, after clonidine injection, the low EMG activity level at baseline was further decreased by 20–30% in parallel to a decrease of mHR although the heterogeneity of the activity ratio remained unaltered. The results suggest that the maintenance of the activity level for the antagonistic jaw muscles are regulated by the distinct physiological mechanisms reflecting the behavioral states during conscious chewing and unconscious NREM sleep.