This study attempts to start up partial nitrification in a sequencing batch biofilm reactor (SBBR) producing an influent suitable for the anammox process and investigate the emission of nitrous oxide (N2O). After 31 days of operation, partial nitrification was achieved at (35 +/- 1) degrees C under intermittently aerated. Based on long-term monitoring, about (1.50 +/- 0.22, n = 5)% of the incoming nitrogen, loaded to the partial nitrification system, was emitted as N2O. The dynamic behavior of N2O emission (quantity (y) varying with time (chi)) in the partial nitrification process can be fit to a line where y = 0.0375x + 0.4806, R-2 = 0.9949. Furthermore, the molecular ecology using polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) techniques was studied, Arcobacter and Nitrospira were washed out during to the controlled aeration and high temperature. Acidobacteria, Cytophagales and Hyphomicrobiaceae were enriched after long term operation of the partial nitrification. Nitrosospira was the dominant AOB causing nitrous oxide emission via a nitrifier denitrification pathway. (C) 2012 Elsevier B.V. All rights reserved.