Automated system documentation generation

A transaction is initiated that involves a plurality of software components in a system. Transaction data is received from a plurality of agents instrumented on at least a subset of software components in the plurality of software components, the transaction data describing attributes of a plurality of fragments of the transaction observed by the plurality of agents. Each transaction fragment includes a respective request and a corresponding response communicated between two software components in the plurality of software components. From the transaction data, a flow of the transaction is determined that describes an order of the transaction fragments and involvement of respective software components in each transaction fragment. Documentation is generated from the transaction data, the documentation describing the system and including a representation of a functional architecture of the system based on the determined flow.