Pectenotoxin-2 seco acid (PTX2sa) and 7-epi-pectenotoxin-2 seco acid (7-epi-PTX2sa) were found in Portuguese shellfish both by fluorescence detection after ADAM derivatisation and, liquid chromatography coupled with mass spectrometry detection. Two time-series both with blue mussel (Mytilus edulis) and common cockle (Cerastoderma edule) from Aveiro lagoon illustrate how PTX2sa has a strong association with Dinophysis acuta occurrence in the plankton, as well as Dinophysis fortii. Data so far excludes D. acuminata from contributing to contamination with pectenotoxins. It also shows that mussel may not be the best indicator of contamination with PTX2sa. At Aveiro lagoon also oyster, razor clam and clams were all less toxic than cockle. Pectenotoxin-2 seco acid was not involved in a previously reported incident of human poisoning that took place in February 1998 after consumption of Donax trunculus. In plankton extracts the most abundant pectenotoxin found was PTX2. Concentration of PTX2sa was around 10% of PTX2, and 7-epi-PTX2sa was not detected.