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Building an optical filtration function into a microfluidic chip is a promising way of simplifying the optical detection system of a microfluidic device. In this paper, a PDMS microfluidic chip filter that is capable of transmitting chlorophyll fluorescence and blocking interfering light in the visible wavelength range was developed for living algae detection with a smartphone. The chip was fabricated by sealing a layer of crystal violet solution in a PDMS layer on the top of the Sudan II-doped PDMS slab, which has a straight microchannel. Optimum dye concentrations and thicknesses for the crystal violet solution layer and Sudan II-doped PDMS slab were investigated and determined by spectrum measurements. It was found that the cut-on range of this integrated microfluidic chip is extended to about 625 nm and the transmittance in the chlorophyll fluorescence range (650 nm to 710 nm) is as high as 95%, when 25 mg L−1 Sudan II-doped PDMS slab (with a 3 mm thickness) and 2 mg L−1 crystal violet solution (with a 0.3 mm thickness) were used. Living algae detection using this chlorophyll-fluorescence-filtering PDMS microfluidic chip and a smartphone-based imaging platform was achieved, and the results compared favorably with those using a commercial filter. [ABSTRACT FROM AUTHOR]