Diatoms can be used as biosensors to assess aquatic environment quality, because they are widely distributed in almost all aquatic environments and show varied sensitivities toward heavy metal ions. The marine planktonic diatoms Phaeodactylum tricornutum (P. tricornutum) and Cylindrotheca fusiformis (C. fusiformis) are typical representatives of planktonic diatoms and benthic diatoms, respectively. C. fusiformis is very sensitive to changes in the concentration of heavy metal ions, and can be used as an indicator of the quality of the sedimental environment, while P. tricornutum can tolerate higher concentrations of heavy metal ions. To explore the potential difference in responses to heavy metal ions between planktonic and benthic diatoms, we compared the transcriptome of P. tricornutum and C. fusiformis under Cu2+ and Zn2+ treatment. The results indicated that P. tricornutum has several genes involved in ion transmembrane transport and ion homeostasis, which are significantly downregulated under Cu2+ and Zn2+ treatment. However, this enrichment of ion transmembrane transport- and ion homeostasis-related genes was not observed in C. fusiformis under Cu2+ and Zn2+ treatment. Additionally, genes related to heavy metal ion stress response such as peroxiredoxin, peroxidase, catalase, glutathione metabolism, phytochelatin, oxidative stress and disulfide reductase, were upregulated in P. tricornutum under Cu2+ and Zn2+ treatment, whereas most of them were downregulated in C. fusiformis under Cu2+ and Zn2+ treatment. This difference in gene expression may be responsible for the difference in sensitivity to heavy metals between P. tricornutum and C. fusiformis.