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The effect of cyanide (CN-) on nitrification was examined with samples from nitrifying bacterial enrichments using two different approaches: by measuring substrate (ammonia) specific oxygen uptake rates (SOUR), and by using RT-qPCR to quantify the transcripts of functional genes involved in nitrification. The nitrifying bioreactor was operated as a continuous reactor with a 24h hydraulic retention time. The samples were exposed in batch vessels to cyanide for a period of 12h. The concentrations of CN- used in the batch assays were 003, 006, 01 and 10mgl(-1). There was considerable decrease in SOUR with increasing dosages of CN-. A decrease of more than 50% in nitrification activity was observed at 01mgl(-1) CN-. Based on the RT-qPCR data, there was notable reduction in the transcript levels of amoA and hao for increasing CN- dosage, which corresponded well with the ammonia oxidation activity measured via SOUR. The inhibitory effect of cyanide may be attributed to the affinity of cyanide to bind ferric haeme proteins, which disrupt protein structure and function. The correspondence between the relative expression offunctional genes and SOUR shown in this study demonstrates the efficacy of RNA-based function-specific assays for better understanding of the effect oftoxic compounds on nitrification activity in wastewater.