BEIS2 (Biogenic Emissions Inventory System version 2) and BEIS3.12 (BEIS version 3.12) were used to estimate hourly biogenic emissions over South Korea using a set of vegetation and meteorological data simulated with the MM5 (Mesoscale Model version 5). Two biogenic emission models utilized different emission factors and showed different responses to solar radiations, resulting in about $10{sim}20%$ difference in the nationwide isoprene emission estimates. Among the 11-vegetation classes, it was found that mixed forest and deciduous forest are the most important vegetation classes producing isoprene emissions over South Korea comprising ${sim}90%$ of the total. The simulated isoprene concentrations over Seoul metropolitan area show that diurnal and daily variations match relatively well with the PAMS (Photochemical Air Monitoring Station) measurements during the period of June 3${sim}$June 10, 2004. Compared to BEIS2, BEIS3.12 yielded ${sim}35%$ higher isoprene concentrations during daytime and presented better matches to the high peaks observed over the Seoul area. This study showed that the importance of vegetation data and emission factors to estimate biogenic emissions. Thus, it is expected to improve domestic vegetation categories and emission factors in order to better represent biogenic emissions over South Korea.