Alexandrium minutum is a toxic dinoflagellate with numerous strains known to produce paralytic shellfish toxins (PSTs). Given the ecological importance and socio-economic impact of A. minutum blooms in coastal waters worldwide, this study assesses the genomic diversity by analysing clonal cultures obtained from an exceptional A. minutum red tide event that occurred in the Ría de Vigo (NW Atlantic coast of Spain) in 2018. To our knowledge this is the first time that satellite DNAs (satDNAs) has been used as chromosomal markers by fluorescence in situ hybridization (FISH) to analyse genomic diversity in a bloom. AmSat002-6, which is monomorphic, and AmiSat017-88 and AmiSat059-512, which colocalized with 45S rDNA can be used as markers to investigate the role of sexuality and its potential role in blooms and other factors that may influence the life cycle of A. minutum. Four satDNAs (AmiSat021-510, AmiSat041-75, AmiSat048-3-AAG and AmiSat060-65) are polymorphic and were used to genotype twelve clonal strains isolated from seven sites over three weeks. In addition, three A. minutum strains from different Mediterranean origins were genotyped. Each strain was distinguished by its unique four-satDNA genotype. Clustering and similarity analyses did not reveal any spatial or temporal grouping of the bloom strains
the dispersion was even greater than the dispersion among the Mediterranean strains, which lay between the bloom strains. The differences in the FISH patterns of sat-DNA within A. minutum may contribute to the assessment of genus diversification.