This review is to talk about an advanced method applied in a totally new field. Since 1960s, algae have been applied as sensitive potential indicators of environment. On the other hand, nanotechnology is a relatively new term to us, and what’s more, its toxicological research is a newborn topic today. Though handful of papers focused on nanomaterial toxicity to human cells and fish were reported, there is no reference on nanotechnology-based toxicological environmental assessments. In this study, the advantages of using algae as indicators for nanotechnology-based toxicity and some molecular biomarkers and methods were discussed and evaluated.