Whereas for extra-tropical regions model estimates of the emission of volatile organic compounds (VOC) predict strong responses to the strong annual cycles of foliar biomass, light intensity and temperature, the tropical regions stand out as a dominant source year round, with only little variability mainly due to the annual cycle of foliar biomass of drought-deciduous trees. As part of the Large Scale Biosphere Atmosphere Experiment in Amazônia (LBA-EUSTACH), a remote secondary tropical forest site was visited in the dry-to-wet season transition campaign, and the trace gas exchange of a strong isoprene emitter and a monoterpene emitter are compared to the wet-to-dry season transition investigations reported earlier. Strong seasonal differences of the emission capacity were observed. The standard emission factor for isoprene emission of young mature leaves of Hymenaea courbaril was about twofold in the end of the dry season (111.5 μgC g−1 h−1 or 41.2 nmol m−2 s−1) compared to old mature leaves investigated in the end of the wet season (45.4 μgC g−1 h−1 or 24.9 nmol m−2 s−1). Standardized monoterpene emission rate of Apeiba tibourbou were 2.1 and 3.6 μgC g−1 h−1 (or 0.3 and 0.8 nmol m−2 s-1), respectively. This change in species-specific VOC emission capacity was mirrored by a concurrent change in the ambient mixing ratios. The growth conditions vary less in tropical areas than in temperate regions of the world, and the seasonal differences in emission strength could not be reconciled solely with meteorological data of instantaneous light intensity and temperature. Hence the inadequacy of using a single standard emission factor to represent an entire seasonal cycle is apparent. Among a host of other potential factors, including the leaf developmental stage, water and nutrient status, and abiotic stresses like the oxidative capacity of the ambient air, predominantly the long-term growth temperature may be applied to predict the seasonal variability of the isoprene emission capacity. The dry season isoprene emission rates of H. courbaril measured at the canopy top were also compared to isoprene emissions of the shade-adapted species Sorocea guilleminiana growing in the understory. Despite the difference in VOC emission composition and canopy position, one common algorithm was able to predict the diel emission pattern of all three tree species.