In recent years the marine environment has been seriously damaged by the presence of several toxic phytoplanktonic species, such as dinoflagellates and other toxic algae, which contaminate shellfish and other marine products. Amnesic and paralytic shellfish toxins are examples of these contaminants. The search for sensitive methodologies for the analysis of such compounds is one of the aims of researchers working in the marine environment. High-performance liquid chromatographic methods have been used for this purpose, allowing the detection of very low levels of these toxins. Recently, capillary electrophoresis (CE) has been used as an alternative for the separation and analysis of these compounds. In this paper, we report the optimization of CE procedures for their analysis. Due to the complexity of the matrix, clean-up procedures are required for removing interferences which affect the electrophoretic resolution. The influences of electrophoretic parameters such as voltage, buffer concentrations and organic modifiers, were studied in order to optimize the electrophoretic system to achieve high resolution as well as an accurate quantitation. Extraction and other steps such as clean-up of samples prior to the electrophoretic analysis have been also studied. Different buffers and organic modifiers were used in order to improve the separation of the toxic components, and consequently to obtain accurate quantitative information about the amount of toxins present in the contaminated samples.