Two large earthquakes (Mw7.3 and Mw7.5) occurred off-shore of the Kii peninsula (Japan) on 5th September 2004. The insufficient station coverage in the area where the large events and their aftershocks occurred led to significant uncertainty regarding their depth location. By using a double-difference approach, we were able to determine more accurate hypocenter locations and better define the main characteristics of the aftershock distribution. The data we used in this study comprise of about 700 earthquakes recorded by the Japanese Meteorological Agency (JMA) from 5 to 12 September 2004. We assume several depth ranges for the initial double difference earthquake locations and select the solution with the smallest rms residual. The resulting hypocenter distribution has two distinctive features: 1) on average the depths are about 20 km shallower than the initial JMA location and 2) the hypocenters are divided into two groups: one shallow (around 12 km depth) and another deep (around 27 km depth). The epicenters of the relocated events define a finer, more clustered structure compared with the epicentral distribution of JMA. The splitting of the earthquake locations into two depth groups is still observed when using a significantly different velocity structure. Our results of the two depth groups for the hypocenters resemble the independently determined hypocentral distribution from the OBS survey.