Identification and enumeration of harmful and potentially toxic phytoplankton species from water samples collected weekly in shellfish production areas, coastal and transition in mainland Portugal since the year 2014. These analyzes are part of the national system of monitoring bivalve mollusc production areas of IPMA and are considered in the zoning and in making decisions regarding their status. The data is collected for the requirements of Regulation (EC) No 854/2004 of the European Parliament and of the Council of 29 April 2004.