Pseudo-nitzschia multiseries is a diatom known for producing domoic acid (DA), a neurotoxin that can cause Amnesic Shellfish Poisoning (ASP), which poses risks to both marine life and human health. This study reports the first detailed investigation of P. multiseries in the Sea of Marmara, focusing on its morphology, phylogeny, and toxin production. Morphological analysis using light and electron microscopy confirmed key diagnostic features consistent with P. multiseries. Phylogenetic analysis, focusing on ITS and LSU gene sequences, showed a close genetic relationship between the Turkish strain and other strains of P. multiseries. Domoic acid levels, quantified using LC-MS/MS during exponential and stationary growth phases, ranged between 2.46 and 3.24 pg cell−1, with minor amounts of isoDA (A, D and E) also detected. These findings highlight the importance of monitoring P. multiseries in Turkish coastal waters due to its significant potential for DA production. This study provides valuable insights into the morphology, phylogeny, and toxin production of P. multiseries, as well as its potential implications for management of marine resources and public health protection. It offers a comprehensive examination of this potentially toxic diatom species in Turkish coastal waters.