The extraction of pigment characteristic spectra from the phytoplankton absorption spectrum has high application value in phytoplankton identification and classification and in quantitative extraction of pigment concentrations. Derivative analysis, which has been widely used in this field, is easily interfered with by noisy signals and the selection of the derivative step, resulting in the loss and distortion of the pigment characteristic spectra. In this study, a method based on the one-dimensional discrete wavelet transform (DWT) was proposed to extract the pigment characteristic spectra of phytoplankton. DWT and derivative analysis were applied simultaneously to the phytoplankton absorption spectra of 6 phyla (Dinophyta, Bacillariophyta, Haptophyta, Chlorophyta, Cyanophyta, and Prochlorophyta) to verify the effectiveness of DWT in the extraction of pigment characteristic spectra.