A system and methods are provided for distributed tracing in a distributed application. In one embodiment, a method includes observing a plurality of messages sent and received among components of the distributed application, generating a probabilistic model of a call flow from observed messages of the distributed system, and constructing a call flow graph based on the probabilistic model for the distributed application. Distributed tracing may include observing messages by performing the subscription-based observation techniques and operations to receive, message traces describing messages being communicated among components of the distributed application. In this regard, the tracing service may merge message traces from different instrumentation points with message traces obtained by observing message queues to generate a probabilistic model and call flow graph. A distributed application developer or other relevant user may benefit in efficiently and effectively tracking down a cause of an abnormal behavior or analyzing performance profiles.