The ways in which bacteria interact with eukaryotic, unicellular algae are extremely diverse. Such relationships vary widely according to a number of criteria, including spatial and temporal scales, the degree of specificity, and if the relationship can be characterized as beneficial or detrimental to any of the organisms involved. These criteria can be applied to our assessment of how microbes interact with those species involved in the formation of harmful algal blooms (HABs). The aim of this paper is to assess the current state of our knowledge of bacterial/HAB interactions as they pertain to the influence of bacteria on HAB population dynamics, the role of bacteria in the production of toxins normally attributed to the algae, and the suggestion that HABs may act as vectors for pathogenic bacteria. Given that viruses are now considered to play a potentially important role in structuring phytoplankton communities, the possible effects of viruses on the population dynamics of harmful algal species are also addressed.