Identifying malicious software provides great benefit for distributed and networked systems. Traditional real-time malware detection has relied on using signatures and string matching. However, string signatures ineffectively deal with polymorphic malware variants. Control flow has been proposed as an alternative signature that can be identified across such variants. This paper proposes a novel classification system to detect polymorphic variants using flowgraphs. We propose using an existing heuristic flowgraph matching algorithm to estimate graph isomorphisms. Moreover, we can determine similarity between programs by identifying the underlying isomorphic flowgraphs. A high similarity between the query program and known malware identifies a variant. To demonstrate the effectiveness and efficiency of our flowgraph based classification, we compare it to alternate algorithms, and evaluate the system using real and synthetic malware. The evaluation shows our system accurately detects real malware, performs efficiently, and is scalable. These performance characteristics enable real-time use on an intermediary node such as an Email gateway, or on the endhost.