With local observed emission factor and meteorological data, this study constrained the Model of Emissions of Gases and Aerosols from Nature (MEGAN) v2.1 to estimate isoprene emission from the Dinghushan forest during fall 2008 and quantify the uncertainties associated with MEGAN parameters using Monte Carlo approach. Compared with observation-based isoprene emission data originated from a campaign during this period at this site, the local constrained MEGAN tends to reproduce the diurnal variations and magnitude of isoprene emission reasonably well, with correlation coefficient of 0.7 and mean bias of 47.5%. The results also indicate high uncertainties in isoprene emission estimated, with the relative error varied from -89.0-111.0% at the 95% confidence interval. The key uncertainty sources include emission factors, γTLD, photosynthetically active radiation (PAR) and temperature. This implies that accurate input of emission factor, PAR and temperature is a key approach to reduce uncertainties in isoprene emission estimation. © 2014 Elsevier Ltd.