<p>Chemotaxonomy, based on pigment markers, has significantly enhanced the monitoring efficiency of phytoplankton assemblages. The quality of the results from chemotaxonomy based on pigment profiles is directly related to the performance achieved in the chromatographic process. HPLC methods described in the literature differ in resolution, sensitivity, and rapidity on the basis of the type of stationary phase and mobile phase used. The objective of this work is to compare the chromatographic performance of a column with porous shell technology particles with a column with totally porous particles, in the separation of phytoplankton pigments by HPLC. To evaluate the efficiency of the chromatographic column, analyses were carried out using a mixed standard containing 26 pigments and revealed greater resolution and peak shape than those obtained with a column made up of totally porous particles. The efficiency of a column with porous shell particles in separating phytopigments was higher than that of a column with totally porous particles, showing greater resolution and symmetry of the chromatographic peaks, especially for the pairs diadinoxanthin/dinoxanthin, divinyl chlorophyll <i>b</i>/chlorophyll <i>b</i> and divinyl chlorophyll <i>a</i>/chlorophyll <i>a</i>. Studies of the reproducibility of the method were carried out using oceanic samples. The resolution of the pair divinyl chlorophyll <i>a</i>/chlorophyll <i>a</i>, an important cyanobacterial marker, was two times higher in the porous shell column, reducing errors in the quantification of important taxonomic markers and securing the success of pigment-based chemotaxonomy.</p>