Due to the scarcity of observational constraints and the rapidly changing environment in East and Southeast Asia, isoprene emissions predicted by models are expected to bear substantial uncertainties. The aim of this study is to improve upon the existing bottom-up estimates, and to investigate the temporal evolution of the fluxes in Asia over 1979–2012. To this purpose, we calculate the hourly emissions at 0.5°×0.5° resolution using the MEGAN–MOHYCAN model driven by ECMWF ERA-Interim climatology. In order to remedy for known biases identified in previous studies, and to improve the simulation of interannual variability and trends in emissions, this study incorporates (i) changes in land use, including the rapid expansion of oil palms, (ii) meteorological variability according to ERA-Interim, (iii) long-term changes in solar radiation (dimming/brightening) constrained by surface network radiation measurements, and (iv) recent experimental evidence that South Asian tropical forests are much weaker isoprene emitters than previously assumed, and on the other hand, that oil palms have a strong isoprene emission capacity. These effects lead to a significant lowering (factor of 2) in the total isoprene fluxes over the studied domain, and to emission reductions reaching a factor of 3.5 in Southeast Asia. The bottom-up annual isoprene emissions for 2005 are estimated at 7.0, 4.8, 8.3, and 2.9 Tg in China, India, Indonesia and Malaysia, respectively. The isoprene flux anomaly over the whole domain and studied period is found to be strongly correlated with the Oceanic Niño Index (r = 0.73), with positive (negative) anomalies related to El Niño (La Niña) years. Changes in temperature and solar radiation are the major drivers of the interannual variability and trends in the emissions, except over semi-arid areas such as northwestern China, Pakistan and Kazakhstan, where soil moisture is by far the main cause of interannual emission changes. In our base simulation, annual positive flux trends of 0.2% and 0.52% throughout the entire period are found in Asia and China, respectively, related to a positive trend in temperature and solar radiation. The impact of oil palm expansion in Indonesia and Malaysia is to enhance the trends over that region, e.g., from 1.17% to 1.5% in 1979–2005 in Malaysia. A negative emission trend is derived in India (−0.4%), owing to the negative trend in solar radiation data associated with the strong dimming effect likely due to increasing aerosol loadings. The bottom-up emissions are compared to field campaign measurements in Borneo and South China and further evaluated against top-down isoprene emission estimates constrained by GOME-2/MetOp-A formaldehyde columns through 2007–2012. The satellite-based estimates appear to support our assumptions, and confirm the lower emission rate in tropical forests of Indonesia and Malaysia. Additional flux measurements are clearly needed to characterize the spatial variability of emission factors better. Finally, a decreasing trend in the inferred top-down Chinese emissions since 2007 is in line with recorded cooling in China after that year, thus suggesting that the satellite HCHO columns are able to capture climate-induced changes in emissions.