Protoceratium reticulatum is a dinoflagellate with a life cycle that includes a motile planktonic stage and a resting cyst stage in benthic habitat, both with a wide geographical distribution, including southern South America. P. reticulatum produces yessotoxins (YTX) – these can be accumulated in shellfish and show potent cytotoxicity, posing a risk to human health if contaminated shellfish is consumed. YTX have been reported from coastal shellfish of many localities, but until now it was unknown if they were present in the austral Southwestern Atlantic and also if local populations of P. reticulatum have the ability to produce these toxins. In this study we report the presence of YTX in plankton samples and its production in culture by two P. reticulatum strains isolated from the San Jorge Gulf (SJG). In addition, we describe the geographical distribution and seasonal abundance of this species based on data collected over the past two decades. The YTX cell quotas calculated from net hauls (∼10 pg cell−1) are in the same range as the toxin cell quotas observed in these two isolates. The phylogenetic analysis of sequences of the hypervariable region of the large subunit (LSU) 28S rDNA showed that the two clonal strains from the SJG were part of a monophyletic clade that subdivides P. reticulatum into two well-supported, divergent sub-clades. The sequences of the two strains of P. reticulatum from the SJG fell in the same clade as the majority of sequences of P. reticulatum, which belong to a geographically widely distributed evolutionary clade. P. reticulatum was occasionally observed from about 35° S in Uruguayan shelf waters up to 53° S on the Patagonian shelf and north of Tierra del Fuego, and it was present from coastal areas up to the shelf break zone. We recorded P. reticulatum in plankton samples during spring, summer and autumn but invariably in low abundance (maximum: 560 cells L−1). Viable cysts of the species in surface sediments also showed a wide geographical distribution. Together, the high total abundances and high relative numerical contribution to planktonic dinoflagellate assemblages near frontal areas, emphasize the necessity to pay attention to the dynamics of this species in areas of potential risk of harmful algal bloom development.