In modern electronic warfare, physical layer security threats have evolved from traditional jammers to smart jammers. Smart jammers, due to their stealthy nature, make wireless communication systems vulnerable. They can easily deceive an Intrusion Detection System (IDS). Cyber security mainly concerns with Confidentiality, Integrity and Availability (CIA). Traditional jammers block availability of communication system whereas smart jammers disturb integrity with false availability. In this thesis, a physical layer intrusion detection system for Direct Sequence Spread Spectrum (DSSS) systems is developed against smart jammers to care about integrity and availability issues caused by smart jammers. Smart jammingnoiseismodeledaswidesensestationary,additiveandcolored. Thisrandomprocess is decomposed into a series expansion of independent and uncorrelated random variables. The decomposition helps in designing a signal-processing algorithm for Physical Layer Intrusion Detection System (PLIDS). The algorithm is easily implemented via correlators. PLIDS is evaluated using simulated electronic warfare environment and its performance is measured in terms of detection capability, precision and accuracy. By adjusting the tuning parameter, error free detection is possible. Different performance tradeoffs are observed for different values of tuning parameter. Finally, asymptotic analysis of proposed PLIDS is performed in terms of time complexity, space complexity and input scale. PLIDS helps detection of smart jammers at physical layer instead of its usual place, i.e., conventional detection using IDS installed at higher layers of TCP/IP protocol stack.