Molecular probes are useful to separate closely related harmful algal bloom species. Moreover, they can rapidly and clearly differentiate nontoxic from toxic algae and to monitor the development of algal blooms in coastal water s. There are three kinds of molecular probes which can be used for identification of HAB species, such as lectin, DNA and peptide nucleotide acid(PNA) probe. These probes are relatively new, and have higher sensitivity, veracity and specificity than traditional taxonomic techniques. In the present study, probes of oligonucleotide, lectin and PNA were applied to detect Prorocentrum minimum, Takayama pulchellum and Alexandrium tamarense of red t ide samples from the East China Sea, Eastern Fujian Coastal Waters and Xiamen Bay, series of studies were undertaken in order to identify and classify these harmful algal species, and the sample processing and detection protocols were evaluated and optimized both in the laboratory and in the field. The results showed that target species of A. tamarense was detected successfully in amples of the East China Sea and Xiamen Bay, and the detection efficiency of different probes specific to A. tamarense was in order: DBA (lectin) > Tama28 S (oligonucleotide probe) > Tama5S(oligonucleotide probe). The target species of P. minimum, was also detected successfully in samples of Eastern Fujian Coastal Waters and Xiamen Bay, and the detection efficiency of different probes specific to P. minimum was as follow: ConA (lectin) > PM18S02 (oligonucleotide) > PM28S02 (oligonucleotide). The target species of T. pulchellum, which was firstly isolated and unialgal cultivated during blooms in Xiamen Bay in 2003 and 2004, was also identified distinctly in samples of Xiamen Bay during blooms in 2005, and the detection efficiency of different probes specific to T. pulchellum was in this order: WGA (lectin) > PNATP28S01 (PNA) > TP18S02 (oligonucleotide)> TP28S01(oligonucleotide). The conclusions were as follow: These target harmful algae bloom species cells appearance in the East China Sea, Eastern Fujian Coastal Waters and Xiamen Bay identified by three probes were correlated well to prevenient results of references, which suggested that specificity of these probes was good and the detecting methods were accurate and reliable. The specificity of three molecular probes was that PNA probe > oligonucleotide probe > lectin probe in order. Thereby, these probes can be used for monitoring marine population dynamics of P. minimum, T. pulchellum and A. tamarense rapidly in future.