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With tremendous growing interests in Big Data, the performance improvement of Big Data systems becomes more and more important. Among many steps, the first one is to analyze and diagnose performance bottlenecks of the Big Data systems. Currently, there are two major solutions. One is the pure data-driven diagnosis approach, which may be very time-consuming; the other is the rule-based analysis method, which usually requires prior knowledge. For Big Data applications like Spark workloads, we observe that the tasks in the same stages normally execute the same or similar codes on each data partition. On basis of the stage similarity and distributed characteristics of Big Data systems, we analyze the behaviors of the Big Data applications in terms of both system and micro-architectural metrics of each stage. Furthermore, for different performance problems, we propose a hybrid approach that combines prior rules and machine leing algorithms to detect performance anomalies, such as straggler tasks, task assignment imbalance, data skew, abnormal nodes and outlier metrics. Following this methodology, we design and implement a lightweight, extensible tool, named HybridTune, and measure the overhead and anomaly detection effectiveness of HybridTune using the BigDataBench benchmarks. Our experiments show that the overhead of HybridTune is only 5％, and the accuracy of outlier detection algorithm reaches up to 93％. Finally, we report several use cases diagnosing Spark and Hadoop workloads using BigDataBench, which demonstrates the potential use of HybridTune.