The effectiveness of two HPLC methods (a monomeric C-18 column with a high ion strength solvent gradient and a monomeric C-8 column with a pyridine-containing mobile phase) in the separation, identification, and quantification of pigments are compared, using phytoplankton, microphytobenthos, and algal cultures. Although the two studied methods showed good analytical resolution, the C-18 method presents a higher discrimination for several carotenoid pigments. On the other hand, the C-8 method allows the separation of chlorophylls c(1), c(2), and Mg-2, 4-divinyl phaeoporphyrin a(5) monomethyl ester as well as the pair chlorophyll a(5) divinyl Chl a. The C-18 method had a shorter elution program and a lower solvent flow rate, making it cheaper and faster than the C-8 method. Furthermore, the C-18 method showed significantly lower detection and quantification limits, a particularly important advantage for pigments present in trace amounts in both phytoplankton and microphytobenthic samples. Differences in the sensitivity of the two studied methods were due mainly to differences in flow rate, with significantly higher peak areas for slower flow rates. No method is ideal for all pigments and sample types and the choice of method should be made in accordance with the objective of each study, taking into consideration the advantages and disadvantages identified for each method.