Marine algae provide a unique niche termed the phycosphere for microorganism inhabitation. The phycosphere environment is an important niche for mutualistic and competitive interactions between algae and bacteria. Quorum sensing (QS) serves as a gene regulatory system in the microbial biosphere that allows bacteria to sense the population density with signaling molecules, such as acyl-homoserine lactone (AHL), and adapt their physiological activities to their surroundings. Understanding the QS system is important to elucidate the interactions between algal-associated microbial communities in the phycosphere condition. In this study, we isolated an epidermal bacterium (ST2) from the marine dinoflagellate Scrippsiella trochoidea and evaluated its AHL production profile. Strain ST2 was classified as a member of the genus Citrobacter closely related to Citrobacter freundii by 16S rRNA gene sequence analysis. Thin-layer chromatography revealed that C. freundii ST2 secreted three active AHL compounds into the culture supernatant. Specific compounds, such as N-butyryl-l-homoserine lactone (C4-AHL), N-octanoyl-dl-homoserine lactone (C8-AHL), and N-decanoyl-dl-homoserine lactone (C10-AHL), were identified by high-resolution tandem mass spectrometry. Carbon metabolic profiling with Biolog EcoPlate (TM) indicated that C. freundii ST2 was widely used as a carbon source and preferred carbohydrates, amino acids, and carboxylic acids as carbon substrates. Our results demonstrated that C. freundii ST2 is a multi-AHL producer that participates in the phycosphere carbon cycle.