Three molecular markers:restriction fragment length polymorphism （RFLP）， random amplified polymorphic （RAPD），amplified fragment length polymorphism （AFLP） are used widely in Populus genetics and breeding studies This paper described basic concept， characteristics， principle，advantages and disadvantages of these markers and also discussed in detail their application and outlook on Populus such as: construct fingerprints， construct genetic linkagemap， genetic variation of population， phylogenetics， evolution and classification， hybrid identification， QTL identification and molecularassisted breeding