Streptomycin is a common contaminant in a variety of industrial and agricultural wastewaters. The available information on the potential toxicity of streptomycin of fresh algae implicated in the treatment of biological wastewater is extremely limited. The objective of this study was to evaluate the effects of streptomycin on physiological indices and photosynthesis-related gene transcription. The results of short-term batch bioassays indicated that streptomycin was more sensitive to cyanobacteria than to green algae. The EC50 of streptomycin in Microcystis aeruginosa and Chlorella vulgaris were 0.28 and 20.08 mg L(-1) , respectively. These selected streptomycin concentrations inhibited algal cell growth and decreased chlorophyll or phycocyanobilin content. Streptomycin also destroyed the overall membrane system, which was speculated from malondialdehyde (MDA) content and electrolyte leakage increasing after streptomycin exposure. Two algae were induced to increase their antioxidant enzyme activities to withstand streptomycin. However, the balance between oxidant substance and antioxidant enzyme was broken, because reactive oxygen species (ROS) content simultaneously increased. Streptomycin inhibited photosynthesis-related gene transcription in C. vulgaris and M. aeruginosa. Transcript levels of psaB, psbA, and rbcL in C. vulgaris decreased to only 14.5%, 32.2%, and 9.3% of the control, respectively. Similarly, the transcript levels of psaB, psbD, and rbcL in M. aeruginosa decreased markedly in the present of streptomycin. The transcription of these genes was 12.4%, 26.1%, and 28.4% of the control after 0.1 mg L(-1) streptomycin exposure, respectively. Our results demonstrate that streptomycin is toxic to fresh algae, affects photosynthesis-related gene transcription, and blocks electron transport and ROS overproduction.