In accordance with an embodiment, described herein are systems and methods for use of a suffix tree to control blocking of blacklisted encrypted domains. A suffix tree includes encrypted hash keys corresponding to a plurality of domain nodes. A domain-related request packet is received, and a target domain name extracted from the packet. A pair of hash keys are generated for the request packet and target domain; and a hash table is searched with the generated hash key pair. If a corresponding entry is found in the hash table, then a corresponding hash suffix pointer is determined for the packet, and the suffix tree examined to determine whether the node identified by the query is part of a blacklisted node. If the suffix tree indicates the node to be part of a blacklisted node, then the system can perform a specified action associated with that node.