Located to the south of East China Sea, the Southern Okinawa Trough (SOT) is a back-arc basin, which belongs to the Ryukyu subduction system. SOT is characterized by an active normal faulting system and numerous volcanic outcrops, which could have marine mineral and geo-hazard potential for its nearby areas. By analyzing the data from the inland Central Weather Bureau Seismic Network (CWBSN) stations, we manually exanimated the waveforms of 2263 earthquakes collected from 1991 to the end of 2011 to identify the possible low frequency (LF) volcanic events. In total, 80 LF earthquakes were recognized. An updated relocation seismicity catalog was used to obtain a more reliable epicenter location. These LF events were mainly located along the central graben of SOT and to the southeast of the Kueishantao (KST) Island. The depths of the LF events are mostly shallower than 15 km near KST, and become deeper when the hypocenters get closer to the central axis of SOT. The LF earthquakes located near KST have relatively higher tendency to occur in cluster with a time interval of 1 to 4 years and the epicenters show a spatial migration. By comparing the distribution of the LF earthquakes with the available geophysical data, we suggest the major faults in SOT do not only influence the distribution for shallow volcanic bodies, but also confine the area of the deep magmatic activity.