The principles and characteristics of several novel molecular markers, SCAR (Sequence Characterized Amplified Region), ISSR (Inter-Simple Sequence Repeat), SRAP (Sequence-Related Amplified Polymorphism) and TRAP (Target Region Amplified Polymorphism), have been described. The application of these markers, in the context of edible mushroom research, has been reviewed. The principles and characteristics of several novel molecular markers, SCAR (Sequence Characterized Amplified Region), ISSR (Inter-Simple Sequence Repeat), SRAP (Sequence- Related Amplified Polymorphism) and TRAP (Target Region Amplified Polymorphism), have been described. The application of these markers, in the context of edible mushroom research, has been reviewed.