The use of HPLC methods to determine and quantify phytoplankton population composition, is sometimes less time-consuming than microscopic identification. However, its general application poses problems since high discrepancies between chlorophyll a calculated using chemotaxonomic methods and direct measurements were noticed. For instance, chemotaxonomic protocols generally employed can lead to a poor estimation of total and relative abundance when high amounts of chlorophyll a breakdown products are present. Therefore, we propose a new approach to calculate relative abundance of algal groups in a phytoplankton population, based on integration of these degradation products in the chemotaxonomic assessment in lentic and shallow freshwater ecosystems.