Harmful algal blooms (HABs), commonly called red tides, are caused by some toxic phytoplanktons, and have made massive economic losses as well as marine environmental disturbances. As an effective and environment-friendly strategy to control HAB outbreaks, biological methods using marine bacteria capable of killing the harmful algae or algicidal extracellular compounds from them have been given attention. A new member of the gamma-Proteobacteria, Hahella chejuensis KCTC 2396, was originally isolated from the Korean seashore for its ability to secrete industrially useful polysaccharides, and was characterized to produce a red pigment. This pigment later was identified as an alkaloid compound, prodigiosin. During the past several decades, prodigiosin has been extensively studied for its medical potential as immunosuppressants and antitumor agents, owing to its antibiotic and cytotoxic activities. The lytic activity of this marvelous molecule against Cochlodinium polykrikoides cells at very low concentrations (1 ppb) was serendipitously detected, making H. chejuensis a strong candidate among the biological agents for HAB control. This review provides a brief overview of algicidal marine bacteria and their products, and describes in detail the algicidal characteristics, biosynthetic process, and genetic regulation of prodigiosin as a model among the compounds active against red-tide organisms from the biochemical and genetic viewpoints.