Using a suitable solvent for extracting pigments from sediment for high performance liquid chromatography(HPLC) analysis is critical for obtaining qualitative and quantitative estimates of phytoplanktonic and benthic algal biomass,as well as community composition. Five methodological factors(sample dehydration,extraction solvent,extraction duration,number of extractions,and ratio of solvent volume:sample weight) were studied using an L 9(3 4 ) orthogonal design in a sedimentary pigment extraction experiment on samples collected from the Changjiang large-river delta-front estuary(LDE),using HPLC analysis. The results show that the optimal extraction method for sedimentary pigments should include freeze-drying samples prior to extraction. The effects of different factors on sedimentary pigment extraction were separated by the L 9(3 4 ) orthogonal design experiments and showed that the extraction solvent was the most important,with extraction duration the second most important,and numbers of extraction and ratio of solvent volume:sample weight was the least important. The mixed solvent treatment comprised of acetone,methanol and water(80:15:5,by volume) was best for polar pigment extraction,with 100% acetone better for apolar pigments. For most pigments employed in this study(i.e.,peridinin,fucoxanthin,alloxanthin,diatoxanthin,zeaxanthin,pheophytin-a and β-carotene) ,3 h was found to be enough time for extraction from these deltaic sediments. However,for chlorophyll-a,the most important pigment used for estimating algal biomass,12 h was needed. A small amount of solvent(3 ml) with duplicate extractions obtained the greatest amount and diversity of pigments. Unfortunately,no extraction method was found to be suitable for all pigments in sediments. The choice of extraction procedure should be made in accordance with the objective of each study,taking into consideration the properties of sediments and pigments in question. Using a suitable solvent for extracting pigments from sediment for high performance liquid chromatography (HPLC) analysis is critical for obtaining qualitative and quantitative estimates of phytoplanktonic and benthic algal biomass, as well as community composition. Five methodological factors (sample dehydration, extraction solvent, extraction duration, number of extractions, and ratio of solvent volume: sample weight) were studied using an L 9 (34) orthogonal design in a sedimentary pigment extraction experiment on samples collected from the Changjiang large-river delta-front estuary using HPLC analysis. The results show that the optimal extraction method for sedimentary pigments should include freeze-drying samples prior to extraction. The effects of different factors on sedimentary pigment extraction were separated by the L 9 (3 4) orthogonal design experiments and showed that the extraction solvent was the most important, with extraction duration the second most important, and numbers of extraction and ratio of solvent volume: sample weight was the least important. The mixed solvent treatment comprised of acetone, methanol and water (80: 15: 5, by volume) was best for polar pigment extraction, with 100% acetone better for apolar For most pigments employed in this study (ie, peridinin, fucoxanthin, alloxanthin, diatoxanthin, zeaxanthin, pheophytin-a and β-carotene), 3 h was found to be enough time for extraction from these deltaic sediments. However, for chlorophyll A, the most important pigment used for estimating algal biomass, 12 h was needed. A small amount of solvent (3 ml) with duplicate extractions obtained the greatest amount and diversity of pigments. Unfortunately, no extraction method was found to be suitable for all pigments in sediments. The choice of extraction procedure should be made in accordance with the objective of each study, taking into consideration the properties of sediments and pigments in question.