To investigate the effects of polycyclic aromatic hydrocarbons (PAHs) and metals on the population reproduction, antioxidative defense system and cell ultrastructure of the marine diatom, fluoranthene and Cu2+ were selected to test their toxicity to Phaeodactylum tricorntum, in the laboratory. The results indicated that both fluoranthene and Cu2+ inhibited population reproduction of P. tricorntum.When the algal cells were exposed to fluoranthene or Cu2+ for 72 h, ultrastructure damage in the cells was observed under a Transmission Electron Microscope (TEM). The chloroplast was a sensitive organelle and the membrane system was very sensitive to the toxicity of fluoranthene or Cu2+. The normal metabolic process might be affected due to cell ultrastructural impairment. However, it needed further investigation to discern whether the ultrastructural damage was responsible for the inhibition of population reproduction.Malondialdehyde (MDA) content indicating oxidative stress was a sensitive index to both fluoranthene and Cu2+ toxicity. Superoxide dismutase (SOD) activity was also a sensitive index to Cu2+ and could be considered as a reference factor in a Cu2+ pollution event, but not in a fluoranthene pollution event.