The toxigenic bloom-forming dinophyte Alexandrium minutum is a globally significant species due to its production of saxitoxins (SXTs), which trigger paralytic shellfish poisoning (PSP) in humans and threaten marine food safety. Despite its ecological and public health relevance, the mechanisms enabling its remarkable bloom persistence and adaptability remain insufficiently understood. In this study, we assessed genetic diversity in natural tropical bloom populations of A. minutum from the semi-enclosed lagoon, Geting Lagoon, Peninsular Malaysia through genotyping using a dual sequencing approach integrating high-throughput sequencing (HTS) of short-read metabarcoding of 18S rDNA region (V7-V9) and long-read Nanopore sequencing of the 18S-28S rDNA region. Ploidy dynamics was inferred through flow cytometric quantification of cellular DNA content. Our findings reveal pronounced genetic polymorphism within bloom populations. High genetic diversity was consistently associated with planozygote- and planomeiocyte subpopulations, whereas vegetative haploid cells exhibited comparatively lower diversity. The results of linkage disequilibrium suggested pervasive sexual reproduction, supporting a dynamic life cycle characterized by incessant excystment and persistent benthic-pelagic coupling. This mechanism enables continuous reseeding of planktonic blooms from benthic reservoirs, sustaining high clonal diversity while constraining population differentiation, as reflected by consistently low F_ST  values. This study highlights the synergistic roles of ploidy transitions and sexual reproduction in shaping the genetic architecture of A. minutum blooms, offering new insights into the mechanisms that support its persistence, adaptability, and evolutionary resilience in tropical marine ecosystems.

Keywords: Alexandrium, cysts, diploid, dormancy, haploid, planomeiocyte, planozygote