As part of the Large Scale Biosphere-Atmosphere Experiment in Amazônia (LBA), we have developed a bottom-up approach for estimating canopy-scale fluxes of isoprene. Estimating isoprene fluxes for a given forest ecosystem requires knowledge of foliar biomass, segregated by species, and the isoprene emission characteristics of the individual tree species comprising the forest. In this study, approximately 38% of 125 tree species examined at six sites in the Brazilian Amazon emitted isoprene. Given logistical difficulties and extremely high species diversity, it was possible to screen only a small percentage of tree species, and we propose a protocol for estimating the emission capacity of unmeasured taxa using a taxonomic approach, in which we assign to an unmeasured genus a value based on the percentage of genera within its plant family which have been shown to emit isoprene. Combining this information with data obtained from 14 tree censuses at four Neotropical forest sites, we have estimated the percentage of isoprene-emitting biomass at each site. The relative contribution of each genus of tree is estimated as the basal area of all trees of that genus divided by the total basal area of the plot. Using this technique, the percentage of isoprene-emitting biomass varied from 20% to 42% (mean = 31%; SD = 8%). Responses of isoprene emission to varying light and temperature, measured on a sun-adapted leaf of mango (Mangifera indica L.), suggest that existing algorithms developed for temperate species are adequate for tropical species as well. Incorporating these algorithms, estimates of isoprene-emitting biomass, isoprene emission capacity, and site foliar biomass into a canopy flux model, canopy-scale fluxes of isoprene were predicted and compared with the above-canopy fluxes measured at two sites. Our bottom-up approach overestimates fluxes by about 50%, but variations in measured fluxes between the two sites are largely explained by observed variation in the amount of isoprene-emitting biomass. © 2004 Blackwell Publishing Ltd.