Boreal forests emit a large amount of monoterpenes into the atmosphere. Traditionally these emissions are assumed to originate as evaporation from large storage pools. Thus, their diurnal cycle would depend mostly on temperature. However, there is indication that a significant part of the monoterpene emission would originate directly from de novo synthesis. By applying 13CO2 fumigation and analyzing the isotope fractions with proton transfer reaction mass spectrometry (PTR-MS) and classical GC-MS, we determined the fractions of monoterpene emissions originating from de novo biosynthesis in Pinus sylvestris (58%), Picea abies (33.5%), Larix decidua (9.8%) and Betula pendula (100%). Application of the observed split between de novo and pool emissions from P. sylvestris in a hybrid emission algorithm resulted in a better description of ecosystem scale monoterpene emissions from a boreal Scots pine forest stand.