In marine ecosystems the interactions among protists and prokaryotes (eubacteria and cyanobacteria) and effects on zooplankton play a dominant role in food web ecology and trophodynamics. Among protists and cyanobacteria, species considered to be harmful algae can cause harm by forming aggregations of cells known as harmful algal blooms (HABs). Certain harmful algae can cause negative ecological effects even at relatively low cell concentrations by production of potent phycotoxins, thereby killing or incapacitating micro-grazers and diverse organisms such as fish, sea-birds and marine mammals by vectorial transfer through marine food webs. Although the ecological role of phycotoxins is poorly understood, the obvious ability of toxic protists to survive, thrive and occasionally to dominate the plankton via the formation of blooms, supports the hypothesis that these bioactive secondary metabolites have a distinct function in the ecological success and evolution of the species.A key component for defining the factors responsible for bloom development is the biochemical and molecular regulation of the toxic and other allelochemical interactions among grazers, prey, and competitors. Knowledge of the genes and enzymes involved in phycotoxin production and their metabolic regulation within the cell, and molecular regulation of other secondary metabolites that may function as allelochemicals, is very limited. Functional genomic and proteomic studies on regulation of phycotoxins/allelochemicals are crucial for our understanding of the molecular ecology of toxigenic microalgae. Studies on genetic regulation and intrinsic control mechanisms of growth and cell proliferation are also required. During the last few years, rapid advances in molecular technologies are allowing us to begin to address this lack of knowledge. Whole genome sequencing and limited genomic approaches, such as expressed sequence tags (ESTs), complemented with the development of DNA-microarrays, are powerful tools to address questions in functional genomics. Application of a spectrum of molecular methods has begun to yield valuable insights into the genetic regulation of processes such as growth and toxin synthesis in marine protists.