ABSTRACTThe Prorocentrales are a diverse group of dinophytes found in a wide range of marine environments. However, species delimitation in the genus Prorocentrum still remains a challenge, especially for nanoscale species where morphological and molecular information is often incomplete. Prorocentrum nux is an example where information is sparse and efforts are needed. In this study, we present a detailed description of the morphological features and molecular information for a Northwest Atlantic strain (AGSB‐0131). Using Scanning Electron Microscopy, additional morphological features from the original description were highlighted, including the periflagellar area configuration (nine vs. seven platelets) and pattern dissimilarities for the large and marginal pores. In addition to the revised description, the 18S rRNA gene, partial 28S rRNA gene, mitochondrial cox1 and cob genes were generated from strain AGSB‐0131, revealing some ambiguity in the existing data available for P. nux. An important genetic divergence between the only 18S rRNA sequence currently available for P. nux (strain RCC303) and AGSB‐0131 was highlighted, suggesting the importance of using the same strain to retrieve morphological and molecular information for nanodinoflagellates. Adding genetic markers for the correct identification of P. nux will enhance the ability to access its prevalence in the marine environment.