Abstract. Biogenic isoprene fluxes were measured onboard the CIRPAS Twin Otter aircraft as part of the California Airborne Biogenic volatile organic compound (BVOC) Emission Research in Natural Ecosystem Transects (CABERNET) campaign during June 2011. The airborne virtual disjunct eddy covariance (AvDEC) approach used measurements from a proton transfer reaction mass spectrometer (PTR–MS) and a wind radome probe to directly determine fluxes of isoprene over 7400 km of flight paths focusing on areas of California predicted to have the largest emissions. The fast Fourier transform (FFT) approach was used to calculate fluxes of isoprene over long transects of more than 15 km, most commonly between 50 and 150 km. The continuous wavelet transformation (CWT) approach was used over the same transects to also calculate instantaneous isoprene fluxes with localization of both frequency and time independent of non-stationarities. Fluxes were generally measured by flying consistently at 400 m ± 50 m (a.g.l.) altitude, and extrapolated to the surface according to the determined flux divergence determined in the racetrack-stacked profiles. The wavelet-derived surface fluxes of isoprene averaged to 2 km spatial resolution showed good correspondence to basal emission factor (BEF) land-cover data sets used to drive BVOC emission models. The surface flux of isoprene was close to zero over Central Valley crops and desert shrublands, but was very high (up to 15 mg m−2 h−1) above oak woodlands, with clear dependence of emissions on temperature and oak density. Isoprene concentrations of up to 8 ppb were observed at aircraft height on the hottest days and over the dominant source regions. Even though the isoprene emissions from agricultural crop regions, shrublands, and coniferous forests were extremely low, observations at the Walnut Grove tower south of Sacramento demonstrate that isoprene oxidation products from the high emitting regions in the surrounding oak woodlands accumulate at night in the residual layer above the valley and mix down into the valley in the morning. Thus, the isoprene emissions surrounding the valley have relevance for the regional photochemistry that is not immediately apparent solely from the direct emission flux distribution. This paper reports the first regional observations of fluxes from specific sources by eddy covariance from an aircraft which can finally constrain statewide isoprene emission inventories used for ozone simulations by state agencies. While previously there was no available means to constrain the biogenic models, our results provide a good understanding of what the major sources of isoprene are in California, their magnitude, and how they are distributed. This data set on isoprene fluxes will be particularly useful for evaluating potential model alternatives which will be dealt with in a separate paper to assess isoprene emission models and their driving variable data sets.