Genistein possesses antibacterial and antioxidant effects. Thermal processing may lead to a decrease of above biological activities of genistein through oxidative degradation. The genistein-encapsulated nanoparticles are prepared by using the techniques of microemulsion and complex coacervation and their surface potential and particle size distribution are analyzed by using dynamic light scattering method. The analysis of Zeta-potential shows that the negative potential difference of surface of nanocapsule significantly increases with the colloid layers increasing and this indicates that the addition of locust bean gum and Arabic gum can increase the negative charges across the nanocapsule surface. The study of particle size distribution suggests that the total average radius of genistein-encapsulated nanoparticles consisted of two particle groups is about 43.7 nm, corresponding to the dispersed single nanocapsule and aggregated nanocapsule, which have the average particle radii of 5.9 nm (72.3%) and 139.9 nm (27.7%). In addition, the total average diameter of nanocapsule is 7.4~10.0 nm at different pH and is not significantly different, but aggregated nanocapsule is found at pH is 6.8 and 7.4.