Novel alga classified instrument based on multi-wavelength LED array is small size, low dissipation,and can achieve on-line, rapid, in situ and classified measure of alga in water. According to characteristics of signal and noise, detection circuit is designed. The experiment indicates that detection limits of microcystis aeruginosa, chlorella vulgaris and nitzschia hantzschiana reach 0.4925 μg/l, 1.9351 μg/l and 0.8686 μg/l respectively, and its linear relation exceed 0.99. The parameters meet requirements of alga measurement in the normal water.