A routing system provides for transparent routing system failover by checkpointing route prefixes during normal operation by maintaining a route prefix table. After failure of a primary routing processor, routing with peer routing systems is synchronized through the use of this prefix table. The prefix table is managed by the primary routing processor and is accessible by a backup routing processor at least after failure of the primary routing processor. Upon the detection of a failure, a backup routing processor solicits routes from peer routing systems in response to the failure and generates a backup routing database from the routes received from peer routing systems. The backup routing processor also compares prefixes of routes in the backup routing database with prefixes in the prefix table, and sends route withdraw messages to the peer routing systems for routes having prefixes listed in the prefix table and not identified in the backup routing database.