We have developed Satellite controller Integrated with Star sensors (SIS) as a prototype of a future small and low-priced satellite controller. To reduce size and cost of the controller, SIS integrates attitude sensors into star sensors with medium resolution and medium sensitivity, adopts Commercial Off-The-Shelf (COTS) electrical parts for key parts such as CPU and CCD, and integrates several electronics for star identification, attitude determination, attitude control, and data handling into a single processing unit. Newly developed computer architecture is introduced for high reliability with COTS parts under the harsh space environment. In this paper, we will focus on the new star identification algorithm dedicated for star sensors with medium resolution and medium sensitivity and evaluate it with in-orbit experiment data of SIS.