Localization is an important function for a mobile robot. In this research, a new localization method using a spherical stereo camera is proposed. Spherical stereo cameras are effective for motion estimation as they can visualize and measure all directions of the environment. Instead of using conventional sparse feature points, dense information of all pixels in images is used to estimate motion accurately. However, because of the wide field of view, the 3D measurement uncertainty is not uniform across the image. Hence, geometric uncertainty of every 3D point is calculated and used as weights to improve accuracy. Experiments show the effectiveness of using uncertainty information to increase the accuracy of motion estimation.