Several ansamycins have been reported to inhibit bacterial biofilm formation and accelerate the eradication of developed biofilms, but little is known about the effect of hygrocin C, an ansamycin, on bacterial biofilm formation. Here, hygrocin C was isolated from the marine-derived Streptomyces sp. SCSGAA 0027 and reported for the first time to be capable of inhibiting the biofilm formation of Staphylococcus aureus and Bacillus amyloliquefaciens SCSGAB0082 with the production of anti-microbial lipopeptides from South China Sea gorgonian Subergorgia suberosa at concentrations of less than minimum inhibitory concentrations. Moreover, hygrocin C also promoted the eradication of developed biofilms, affected the biofilm architecture, and lowered the extracellular polymeric matrix formation, cell motility, and surface hydrophobicity in B. amyloliquefaciens, which was in accordance with the inhibition of biofilm formation. Furthermore, transcriptome analysis revealed that hygrocin C altered the transcripts of several genes associated with bacterial chemotaxis and flagellar, two-component system and the synthesis of arginine and histidine, which are important for bacterial biofilm formation. In conclusion, hygrocin C could be used as a potential biofilm inhibitor against S. aureus and B. amyloliquefaciens. But further genetic investigations are needed to provide more details for elucidation of the molecular mechanisms responsible for the effects of hygrocin C on B. amyloliquefaciens biofilm formation.