Protease produced from Bacillus sp. FSE-68 was isolated from Meju, a Korean fermented soybean starter, and was purified by a two-consecutive aqueous two-phase system. The change of partition coefficient (K) in the polyethylene glycol (PEG)/potassium phosphate buffer (PPB) aqueous two-phase system was measured at different pHs (6.0- 9.2), PPB concentrations (8-12%), and temperatures (4 and $20^{circ}C$). As the PPB concentration in the aqueous two-phase system increased, the protease concentration in the top phase (PEG-rich phase) increased, thereby enhancing the partition coefficient. The minimum partition coefficient of the protease was achieved at pH 7.0, whereas that of the total protein was at pH 6.0. The biggest difference in partition coefficients of total protein and protease occurred at pH 6.0. It was interesting to note that the partition coefficient of protease decreased as the temperature increased. The optimum condition of the primary aqueous two-phase extraction of Bacillus sp. FSE-68 was pH 6.0, 14% (w/w) PPB, and 16% (w/w) PEG at $4^{circ}C$, and the crude enzyme concentration in this system was 50% (w/w). The protease, which was concentrated in the top phase, was further mixed with 15% (w/w) PPB (pH 7.0) in the ratio of 1:1 at $20^{circ}C$ to elute the bottom phase (PPB-rich phase). Using these steps, the purification fold achieved was 9.2 with a 44.7% yield.