Phycotoxin distribution and abundance was determined during an oceanographic expedition along a latitudinal transect of 27° extent in the southeastern Pacific Ocean, from the fjords of Tierra del Fuego Island to offshore Copiapó in the Atacama region along the Chilean coast. Plankton samples were harvested at regular intervals during the entire cruise and later analyzed by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) for domoic acid (DA) and lipophilic toxins. Although no evident toxic algal bloom was encountered during this transect, several phycotoxin analogues from distinct toxin groups were detected. These phycotoxins included DA, the pectenotoxins PTX-2, PTX-2sa and PTX-11, dinophystoxin-1 (DTX-1) and gymnodimine (GYM), which is the first report of this latter toxin in the southeast Pacific. A region-specific and rather disjunct distribution of GYM, DA and DTX-1 was observed, whereas PTX-2, PTX-2sa and PTX-11 were more widely distributed over almost the entire transect. This work represents the first assessment of lipophilic toxins through a wide latitudinal transect of the southeastern Pacific, revealing a patchy distribution of several phycotoxins and pointing out the specific geographical distribution of the putative toxigenic organisms. © 2011 Elsevier Ltd.