Comparisons of microbial community structure, in eight filter media of zeolites, anthracite, shale, vermiculite, ceramic filter media, gravel, steel slag and bio-ceramic, were undertaken by analyzing the phospholipid fatty acid (PLFA) composition. A total of 20 fatty acids in the range of C₁₁ to C₂₀ were determined but only 13 PLFAs were detected in steel slag. They consist of saturated fatty acids, branched fatty acids, monounsaturated fatty acids, and polyunsaturated fatty acids. The variation of fatty acids was revealed in the relative proportions of these fatty acids in different media. The aerobic prokaryotes were the predominant group in all media. The PLFA composition showed significant differences among the eight different media by Tukey's honestly test. It was found that steel slag was significantly different in the microbial community as compared to other filter media, probably due to its alkaline effluent. Steel slag alone is probably not a good choice of substratum in constructed wetlands. The principle components analysis (PCA) showed that zeolites, bio-ceramic, shale and vermiculite had a similar microbial community structure while steel slag and ceramic filter media were distinct from other media.