At low tide, intertidal mudflat biofilms cover large surfaces and are mainly responsible for the high productivity of these marine areas. In the European Atlantic coast, such biofilms are mainly composed of diatoms, especially Navicula phyllepta, bacteria, and microbial extracellular polymeric substances (EPS). To better understand interactions occurring between microorganisms, we first axenized a N. phyllepta culture with a new and simple protocol. Colloidal and bound EPS secreted by diatom cells during the exponential growth and the stationary phase were then harvested, and we tested their effects on the in vitro formation of biofilms by three marine bacteria. The latter had been isolated from a French Atlantic intertidal mudflat and were previously selected for their strong in vitro biofilm-forming ability. They belong to the Flavobacterium, Roseobacter, and Shewanella genera. Navicula phyllepta-bound EPS synthesized during the stationary phase specifically inhibited the biofilm formation by the Flavobacterium sp. strain, whereas they stimulated biofilm development by the two other strains. The EPS acted in all cases during the first stages of the biofilm establishment. Saccharidic molecules were found to be responsible for these activities. This is the first report on marine bacterial antibiofilm saccharides of microalgal origin. This work points out the complexity of the benthic natural biofilms with specific microalgae/bacteria interactions and underlines the possibility to use axenic diatoms as a source of bioactive compounds.