Chlorophyll-a was regarded as the important indicator to describe the marine primary production because the chlorophyll a content of phytoplankton in the ocean is related to its photosynthesis production. The concentration of chlorophyll a is also the major parameter to evaluate marine water quality, organic pollution and detect the fishing ground, and the temporal and spatial variation of chlorophyll a contains the basic information of sea areas. Based on the spectral characteristics of chlorophyll fluorescence, this document recommends a new dual optical detecting instrument for the measurement of chlorophyll-a concentration, the microcontroller MSP430F149 as the key control module, by controlling the ultra-high brightness LED which wavelength is 450nm to excite chlorophyll a to produce the fluorescent signal about 680nm , at the same time this LED is used as reference light, the dual-optical structure exclude the light fluctuations due to the impact of test results. At last, we get the relationship between relative fluorescence intensity and chlorophyll-a concentration with the spectrophotometer, we find the system has the good linear consistency when measures the low concentrations of chlorophyll-a.