Peroxynitrates are responsible for global scale transport of reactive nitrogen. Recent laboratory observations suggest that they may also play an important role in delivery of nutrients to plant canopies. We measured eddy covariance fluxes of total peroxynitrates (ΣPNs) and three individual peroxynitrates (APNs ≡ PAN + PPN + MPAN) over a ponderosa pine forest during the Biosphere Effects on AeRosols and Photochemistry EXperiment 2009 (BEARPEX 2009). Concentrations of these species were also measured at multiple heights above and within the canopy. While the above-canopy daytime concentrations are nearly identical for ΣPNs and APNs, we observed the downward flux of ΣPNs to be 30–60% slower than the flux of APNs. The vertical concentration gradients of ΣPNs and APNs vary with time of day and exhibit different temperature dependencies. These differences can be explained by the production of peroxynitrates other than PAN, PPN, and MPAN within the canopy (presumably as a consequence of biogenic VOC emissions) and upward fluxes of these PN species. The impact of this implied peroxynitrate flux on the interpretation of NOx fluxes and ecosystem N exchange is discussed.