The MEGAN model was used to quantify isoprene emission in the Pearl River Delta (PRD) region for 2006. Two sensitive experiments were conducted in order to investigate the impacts of uncertainties in simulated, meteorological, near-surface weather elements on modeled isoprene emission. The results showed that the annual isoprene emission was 95.56 × 106 kg C in the PRD in 2006. Due to variations of meteorological conditions, the isoprene emission displayed a remarkable seasonal and diurnal variation. The highest seasonal emission flux was in summer with a value of 0.920 t · km-2. Considering diurnal patterns, the highest emission rate was at 13:00 local time. The results of sensitive experiments revealed that errors in MM5-simulated meteorological elements significantly impacted isoprene emission while overestimated (underestimated) solar radiation could increase (decrease) the emission rate by 36.20%~50.70% (30.73%~41.88%), which was larger than changes caused by temperature. However, changes in meteorological inputs did not affect the diurnal pattern of isoprene emission, just the emission rate. The emission rate of isoprene changed mostly at 8:00 in the morning or at 17:00 in the afternoon.