Abstract: Synthetic non-metallic nanoparticles have been explored to treat harmful algal blooms, but their strain-specific algicidal activities have been rarely investigated. Three batches of CNDs were prepared in-house using glucose or chloroform and methanol as the substrate and one batch of single-walled CNTs. The axenic laboratory culture of each cyanobacterial strain was exposed to an NMNP at two dosage levels for 48 h, followed by measurement of five endpoints. The endpoints were optical density at 680 nm for chlorophyll-a estimation, OD at 750 nm for cell density, instantaneous pigment fluorescence emission after being excited with 450 nm blue light for chlorophyll-a or 620 nm red light for phycocyanin, and quantum yield for photosynthesis efficiency of photosystem II. The results indicate the acute toxicity was strain-, NMNP type-, dosage-, and endpoint-dependent. The two benthic strains were more resistant to NMNP treatment. SWCNTs and fraction A14 of CND-G were more toxic than CND-G and CND-C/M. The CPP was the least toxic. The high dose generally caused more severe impairment. OD750 and OD680 were more sensitive and QY was the least sensitive. The strain dependence of toxicity suggested the potential application of these NMNPs as a target-specific tool for mitigating harmful cyanobacterial blooms.