This paper investigates the development of Fault Detection and Isolation (FDI) filters for spacecraft formation flight. A MIMO architecture for formation flying control is considered. By utilizing a geometric FDI methodology, a local/decentralized detection filter is developed for detecting faults in other spacecraft by determining the required unobservability subspace of the local system. In the case when such an unobservability subspace does not exist, the required communication links between the spacecraft are specified. Simulation results presented demonstrate the effectiveness of our proposed methodology for FDI of formation flying systems.