Microcystic aeruginosa was cultivated in laboratory condition with nature water for about 95 days. Three dimensional excitation-emission(3DEEM) fluorescence spectroscopy and synchronous scan fluorescence spectroscopy of the culture water at different growth stages were measured,simultaneously the chlorophyll-a and extracellular MC-LR concentration were analyzed.The results show that fluorescence signal A,signal X and signal C could be observed obviously from 3DEEM fluorescence spectroscopy and synchronous scan fluorescence spectroscopy,which represent protein-like substance,marine humic-like acid and fulvic-like substance respectively.All the three fluorescence signals intensity and MC-LR concentration were normalized by chlorophyll-a concentration.In the decline phase,the normalized fluorescence signals(A,X,C) and normalized MC-LR concentration show the same dynamic laws and good linear correlation.The maximum values appeared at the same time.Therefore,MC-LR concentration can be estimated by the feature fluorescence signal(A, X,C) and chlorophyll-a concentration.Comparing to 3DEEM fluorescence spectroscopy,synchronous scans fluorescence spectroscopy(△λ=80 nm) is less time-consuming and can give out the entire feature fluorescence signal(A,X,C).It is suitable for real-time analysis of water fluorescent spectroscopy which can be used to rapidly estimate the MC-LR concentration.