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A highly sensitive and reliable chlorophyll sensor is proposed and evaluated to meet the demand of in-situ chlorophyll detection. As the major innovation, pseudo-random sequence modulation is introduced into the amplitude measurement of the fluorescence for the first time. Compared with the conventional single frequency square wave modulation, the pseudo-random sequence modulation could spread the spectrum of the fluorescence, and improve the sensitivity and the interference suppression ability of the sensor without increasing the complexity of the system's hardware. The sensitivity experiments show that the sensor could detect chlorophyll as low as 0.0103 μg/L, with the concentration range of 0~25 μg/L and the R-square of 0.9998. In the interference suppression test, for the same interference in the passing band, the maximum response of the 31 bits PRS modulation system is 2.3 times smaller than that of the single frequency square wave modulation system.