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We present Roots, a full-stack monitoring and analysis system for performance anomaly detection and bottleneck identification in cloud platform-as-a-service (PaaS) systems. Roots facilitates application performance monitoring as a core capability of PaaS clouds, and relieves the developers from having to instrument application code. Roots tracks HTTP/S requests to hosted cloud applications and their use of PaaS services. To do so it employs lightweight monitoring of PaaS service interfaces. Roots processes this data in the background using multiple statistical techniques that in combination detect performance anomalies (i.e. violations of service-level objectives). For each anomaly, Roots determines whether the event was caused by a change in the request workload or by a performance bottleneck in a PaaS service. By correlating data collected across different layers of the PaaS, Roots is able to trace high-level performance anomalies to bottlenecks in specific components in the cloud platform. We implement Roots using the AppScale PaaS and evaluate its overhead and accuracy.