As a part of a monitoring program of harmful microalgae in the coastal waters of Buenos Aires Province, two strains of chain-forming Gymnodinium species (Dinophyceae), LPCc043 and LPCc044, were isolated from samples collected in Samborombón Bay. This study aims to provide a morphological, phylogenetic and toxicological characterization of the strains. Among marine chainforming Gymnodinium species, only G. catenatum and G. impudicum are known to form harmful algal blooms (HAB). Morphological analysis with light and electron scanning microscopy (LM, SEM) revealed that strain LPCc043 had larger cells, a higher number of cells per chain, and an acrobase independent of the sulcus entering the epicone, whereas strain LPCc044 had smaller cells, a lower number of cells per chain, and an acrobase as an extension of the sulcus. Phylogenetic analysis based on partial LSU rDNA sequencing placed the sequence corresponding to strain LPCc043 in the G. catenatum clade and that corresponding to strain LPCc044 in the G. impudicum clade with a 99–1.0 and 100–1.0 bootstrap and Bayesian posterior probability, respectively. Toxicological analysis by hydrophilic interaction liquid chromatography with tandem mass spectrometry (HILIC-UHPLC-MS/ MS) detected paralytic shellfish toxins (PSTs) in G. catenatum, predominantly N-sulfocarbamoyl11-hydrosulfate toxin 1/2 (C1/C2) and decarbamoyl gonyautoxin 2/3 (dcGTX2/3). In contrast, no PST were found in G. impudicum. This study contributes to the knowledge of harmful algal species diversity along the Argentinean coast and highlights the importance of monitoring these species for public health and environmental management.