Five strains of Planktothrix agardhii isolated from five regions around China were studied for their physiological characteristics, including growth rate, pigment composition, photosynthetic activity. Strain HAB1128 isolated from Guangzhou contained lower chlorophyll-a(Chl.a), but higher C-PC content and higher C-PC ratio in total phycobiliprotein compared to other 4 strains. Results from electron transfer rate (ETR) showed that HAB1128 had higher photosynthetic ETR and the maximal ETRmax, which inferred that high-performance electron transfer chain retrieved the inadequacy of Chl.a of this strain, and lead to the neutral growth rate. On the contrary, HAB631 the strain isolated from East Lake (Wuhan), contained higher Chl.a content, but showed lower growth rate due to its weak electron transfer chain. No significant differences of physiological parameters were shown among three strains isolated from Beijing, Shanghai and Yunnan.