In this paper, we propose a generic approach to tracking multiple indistinguishable moving targets with wireless sensor networks. The tracking algorithm first separates the aggregate signals from multiple indistinguishable targets via the Blind Source Separation (BSS) method. Through the analysis on both the temporal and the spatial correlation of the separated individual signals, the tracking algorithm determines the real-time location of a target and its moving track. A voting scheme based on the spatial information is designed to better estimate the moving track. Furthermore, we analyze and discuss the influence of signal attenuation and the tracking resolution of the proposed tracking approach. Both empirical experiments and simulations show that the proposed approach can both accurately and precisely track multiple indistinguishable moving targets.