The phospholipid fatty acid (PLFA) composition was analyzed in two red soils experimentally contaminated with copper at different concentrations. The total amounts of phospholipid fatty acids (PLFAs) in both red soils were significantly correlated with soil microbial biomass C and N, which decreased consistently with increasing levels of copper. The relative quantities of the PLFAs 17:0 (10 Me), i16:0, i15:0 and 16:1w5c, decreased with increasing heavy metal concentration, while those of cy17:0, which is an indicator of gram-negative bacteria, increased. The Shannon index calculated from the PLFA data indicated that Cu addition in the red soils decreased the population diversity of soil microbial communities. Multivariate analysis of PLFA data demonstrated that high levels of Cu application had a significant impact on microbial community structure and there is a threshold metal concentration for PLFA composition. Comparatively higher toxic effect on microbial biomass and community structure were found in the red sandy soil than those in the red clayey soil. The differential effect of Cu addition on microbial communities in the two soils may be due to differences in soil texture and cation exchange capacity.