The development of genetics has entered into new genetic markers application ysage which developed one after the other from Mendelian morphological marker, cytogenetics marker, allozyme marker to DNA markers in algal research.Based on morphological features such as the colours and seed sizes of pea, Mendel discovered the famous genetic laws. The cytogenetics markers included chromosome morphology, number and structure, which can be used for gene localization. Allozymes are allelic variants of proteins produced by a single gene locus, and are of interest as markers because of the existing polymorphism. Since the 1970s, it has been used widespread for population genetics and other fields in biology. Since the last decade of the 20th century, various DNA marker techniques have been invented, such as RFLP, RAPD, AFLP, SSR and SNP. With DNA markers, it is conveniently and easily to observe and exploit genetic variation in the entire genome. However, the application of molecular markers is still in its primary level. Here the principles and characters of kinds of molecular markers were reviewed including their applications in algae research, respectively.