The carbon metabolism of microorganisms in biofilters of a recirculating aquaculture system(RAS) cultured with Anguilla marmorata was investigated using Biolog Eco plates.The biofilms were collected from two different tanks of a fluidized bed filter and three different depths of a trickle filter(top,middle and bottom).The results showed that there is no significant difference for Shannon-Wiener index,Simpson index and Pielou index among the biofilms collected from two different tanks of fluidized bed filter and the middle and bottom of trickle filter(P>0.05),all of which was significantly higher than that in the top of the trickle filter(P<0.05).The average well color development(AWCD) and principal component analysis all demonstrated the carbon metabolism of microorganisms in the top of trickle filter was different from other four sample sites.Microorganisms in all sample sites didn't show any preference for any of the six categories of carbon sources.However,the Itaconic acid,D-Galacturonic acid,L-Arginine,L-Asparagine,L-Serine,D-Mannitol,D-xylose,N-Acetyl-D-Glucosamine,Tween 40,Tween 80 and Phenylethyl-amine could be well used by microorganisms from all the sample sites,while γ-Hydroxy butyric acid,α-Ketobutyric acid,D,L-α-Glycerol Phosphate and Glucose-1-Phosphate could not be used by most of microorganisms from all the sample sites.Some carbon sources such as D-Glucosamic Acid,α-D-Lactose,and 2-Hydroxy Benzoic Acid could only be used by microorganisms from certain sample sites.The present study illustrated the properties of carbon metabolism of microorganisms in biofilter of a RAS using Biolog Eco plates and gave a new possibility for water quality control in RAS,which will promote the microbial community changes through regulating the carbon sources in the system to manage the water quality.