One frequently-cited method for determining phycoerythrin (PE) and phycocyanin (PC) contents from crude aqueous extracts of red seaweeds utilizes peaks and troughs of absorbance spectra. The trough absorbance values are used to establish a linear or logarithmic baseline attributable to background scatter of particulate cellular debris not removed by centrifugation. Pigment contents are calculated by subtracting baseline values from PE and PC absorbance peaks. The baseline correction is intended to make the method independent of centrifugation time and/or speed. However, when crude extracts of Porphyra were analyzed using this protocol, R-PE and R-PC estimates were significantly affected by centrifugation time, suggesting that the method was not reliable for the genus. The present study has shown that with sufficient centrifugation, background scatter in Porphyra extracts can be removed, the remaining spectrum representing the overlapping absorbance peaks of water-soluble pigments in the extract. Using fourth derivative analysis of Porphyra extract absorbance spectra, peaks corresponding to chlorophyll, R-PE, R-PC, and allophycocyanin (APC) were identified. Dilute solutions of purified R-PE, R-PC and chlorophyll were scanned separately to identify spectral overlaps and develop new equations for phycobilin quantification. The new equations were used to estimate R-PE and R-PC contents of Porphyra extracts and purified R-PE, R-PC and chlorophyll solutions were mixed according to concentrations corresponding to the sample estimates. Absorbances and fourth derivative spectra of the sample extract and purified pigment mixtures were compared and found to coincide. The newly derived equations are more accurate for determining R-PE and R-PC of Porphyra than previously published methods.