Marine microbial eukaryotes are highly diverse and remain relatively little studied. Genetically, many species are complex, and possess very large genomes. Some species produce secondary metabolites, including biotoxins, which can have harmful impacts on marine biota and humans, if we consume them via shellfish or finfish vectors. Using molecular genetic approaches, my research group has worked to uncover the toxicology, ecology, and phylogeography of marine biotoxin-producing microbial eukaryotes. In this talk, I will discuss examples from the East Australian current region, highlighting the role of genetic tools for harmful algal bloom detection, changing species distributions, and the evolution and ecology of marine biotoxins.