Radio frequency identification (RFID) systems are emerging platforms that support a variety of pervasive applications. RFID tags can be used to label items and enable item-level monitoring. The problem of identifying missing tags in RFID systems has attracted wide attention due to its practical importance (e.g., anti-theft). This paper presents P-MTI: a Physical-layer Missing Tag Identification scheme that effectively makes use of the lower-layer information and dramatically improves operational efficiency. Unlike conventional approaches, P-MTI looks into the aggregated tag responses instead of focusing on individual tag responses and extracts useful information from physical-layer collisions. P-MTI leverages the sparsity of missing tag events and reconstructs tag responses through compressive sensing. We prototype P-MTI using the USRP software defined radio and Intel WISP platform. We also evaluate the performance of P-MTI with extensive simulations and compare to previous approaches. The experiment results show the promising performance of P-MTI in identification accuracy, time efficiency, as well as robustness over noisy channels.