With the strengths of quickness, low cost, and adaptability, unmanned aerial vehicle (UAV) communication is widely utilized in the next-generation wireless network. However, some risks and hidden dangers such as UAV “black flight” disturbances, attacks, and spying incidents lead to the necessity of the real-time supervision of UAVs. A compressed sensing-based genetic Markov localization method is proposed in this paper for two-dimensional trajectory tracking of the mobile transmitter in a finite domain, which consists of three modules: the multi-station sampling module, the reconstruction module, and the localization module. In the multi-station sampling module, multiple stations are deployed to receive the signal transmitted by the UAV using compressed sensing, and the motion model of the mobile transmitter is the constant turn rate and acceleration (CTRA) model. In the reconstruction module, we propose a direct reconstruction method to extract the joint cross-spatial spectrum. In the genetic Markov localization module, we propose a two-step localization method to genetically correct the inaccurate points in the preliminary results and generate the tracking result. Extensive simulations are conducted to verify the effectiveness of the proposed method. The results show that the proposed method is superior to the particle filter method and the Markov Monte Carlo method at all sampling moments. Specifically, when SNR = 15dB, the root-mean-square error (RMSE) of the proposed method is 39% and 60% lower than that of the other two methods, respectively. Moreover, under the premise that the RMSE of the localization result is less than 30 m, the reconstruction module can reduce the running time of the proposed method by 33.3%.