In this microcosm study, we focused on the effect of a combined application of copper and mefenoxam on the functional diversity of soil microbial communities. Treatments with combined and separate applications of copper and mefenoxam were sampled at 24 and 60 days and control soil was sampled at 0, 24 and 60 days. Structural and metabolic profiling of microorganisms were performed by arbitrarily primed (AP) and RNA arbitrarily primed-PCR (RAP-PCR). Cluster analysis resulted in separate grouping of AP and RAP-PCR profiles, with differences between control and treatments being more pronounced with respect to RAP-PCR profiles. amoA, a functional molecular marker for beta-subgroup ammonia-oxidizing bacteria, could only be detected at day 60 in treatments of mefenoxam, and mefenoxam+copper, with higher gene copies in the latter. There was also an increase in potential nitrification activity on application of mefenoxam and mefenoxam+copper. Comparison of amoA diversity was performed by denaturing gradient gel electrophoresis followed by construction of a clone library of amoA fragments amplified from the mefenoxam+copper-treated sample. Analysis of clones was performed by restriction digestion and subsequent sequencing. Patterns 1 and 5 were seen in 93% of the clones and clustered together with amoA sequences of Nitrosospira, indicating that Nitrosospira-like organisms are the major nitrifiers under mefenoxam treatments.