Sulfolobus islandicus is a commonly used type strain to study replication, cell cycle and CRISPR-Cas system in archaea. For this reason, it is important to establish a genetic manipulation system in Sulfolobus islandicus. Here, we describe the plasmid vector, selection marker and transformation methods, and discuss two currently widely used gene knockout systems. Meanwhile, we also address some major problems in genetic manipulation systems of Sulfolobus islandicus, and indicate development prospects.