A system for managing cryptographic keys and trust relationships in a secure shell (SSH) environment by mapping network servers, clients, and appliances and locating SSH keys and key pairs associated with each device. The system provides for mapping the network topology and all SSH keys and key pairs stored on network connected devices, and the creation of a master database of all devices, keys and key pairs, key types and encryption strength, and user accounts with which each key or key pair is associated. The mapping and database enable the effective management of SSH keys and key pairs, detection of errors and weakness, elimination of orphaned or outdated keys, correction of all deficiencies, and replacement of keys in accordance with policies set by the organization maintaining the network.