BIOLOG YT and FF microplates were used in this study to investigate the metabolic activities and similarity of 4 fungal communities in environmental samples. Subsequently, the BIOLOG metabolic similarity expressed by these two microplates was linked to structural similarity expressed by Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE). In addition, the effect of cryopreservation on BIOLOG analytic results, including metabolic activities, richness index and diversity index, was also discussed. The following conclusions have been drawn: (1) BIOLOG FF microplate expressed a metabolic similarity relation among 4 fungal communities absolutely different from that by BIOLOG YT microplate. (2) The BIOLOG FF metabolic similarity of 4 fungal communities nearly corresponded to the PCR-DGGE structural similarity. (3) The cryopreservation had no significant influence on BIOLOG richness index, BIOLOG FF metabolic activities and BIOOG YT diversity index (P > 0.05).