In this study, Marinobacter sp. FL06 was used to effectively harvest the energy-producing microalga Thalassiosira pseudonana through direct flocculation. Strain FL06 showed 92.7% flocculating efficiency against T. pseudonana, and no metal ion was added for the flocculation process, resulting in a more environmentally friendly process. The flocculation efficiency of FL06 was stable over a wide range of pH values and temperatures, indicating that the application of this bacteria has potential advantages under various conditions. Strain FL06 also exhibited flocculation activity against different microalgae, indicating that the strain can be used to harvest multiple types of microalgae. Strain FL06 showed high chemotactic ability toward algal cells, suggesting that chemotaxis is important for flocculation. This study provides the first demonstration that the Marinobacter genus could be used to harvest T. pseudonana biomass. In summary, the results showed that FL06 has the potential for effective harvesting of microalgal biomass.