As the increasing needs of indoor applications, the development of a real time indoor positioning system is essential. The purpose of this paper is to develop a low cost and low power consumption Real Time Indoor Positioning System (RTIPS) and then integrate this RTIPS with a self-developed indoor Geographic Information System (GIS) to form a indoor Location Based Service (LBS) prototype. In this paper we utilize the Wireless Sensor Network (WSN) as our indoor positioning system, and the ZigBee radio is used as our wireless protocol because of its low cost and low power consumption. The positioning algorithm used in this paper is the fingerprinting method which based on the Received Signal Strength (RSS). In this paper we evaluate the positioning results with different matching algorithms including 1) the Nearest Neighbor (NN) algorithm, 2) K-Weighted Nearest Neighbors (KWNN) algorithm with various values of K, and 3) the probabilistic approach based on the kernel method. We also implement the suboptimal filter, the particle filter, to improve the performance of the RTIPS. The trade-off study between the positioning accuracy and the number of particles used in the particle filter will be investigated in this paper. Additionally, to provide the indoor LBS for users, this paper proposes a rapid and efficient procedure to build a 3D indoor Geographic Information System (GIS). This GIS which integrates the Computer-Aided Design (CAD) and the Virtual Reality Modeling Language (VRML) technique is easy to update and maintain in future. In this paper the Department of Aeronautics and Astronautics building at National Cheng Kung University in Taiwan is used to demonstrate a real time indoor LBS prototype which successfully integrates the RTIPS with the self-developed indoor GIS.