With the booming of the genome era, the whole genome sequencing of important filamentous fungi has been basically completed and is widely used in the fields of industry, agriculture and medicine. However, the genetic transformation efficiency of filamentous fungi is extremely low. In order to ensure that positive transformants can be picked out from a large number of non-transformed colonies. Therefore appropriate selectable markers are particularly important. At present, the commonly used selectable markers in the genetic transformation of filamentous fungi can be divided into two categories: drug-resistance selectable markers and auxotrophic selectable markers. However, both of them have distinct limitations. For this reason, researchers use the latest genome editing technology to modify the selectable markers for better genetic selection. This article reviews the current genetic selection system and new screening marker theory modified by genome editing technology, which lays a foundation for a broader application prospect of filamentous fungi in various fields.