Endophytic fungi (EF) are fungal organisms with different levels of living. EF include a blend of fungal group inside plants expended between non-pathogenic to virulent pathogens of fungi and different organisms. Several EF could be fungal pathogens (as facultative parasite or saprophyte) attacking different organisms such as insects, spiders, and nematodes. Generally, the relationship of EF is divided between mutualistic to latent pathogens, but their interaction with plants, depending on the fungal isolate or strain, can lead to different outcomes including: (A) producing natural products, (B) capability to be plant pathogens, and (C) activity as biocontrol agents. This causes confusion and a problem concerning the interaction between fungal isolate/s and plants as this can be useful or harmful. Finally, the activity of fungal isolates and their relationship with plants is dependent on the gene of fungal isolate, the environmental conditions, as well as the interaction between the gene and environment.