A photoacoustic spectrometer for the simultaneous detection of isoprene and the deuterated species [4,4-2H]-2-methyl-1,3-butadiene (isoprene-d2) is presented. Using a sealed-off 13CO2 laser a single-component detection limit of 400 ppt (isoprene) and 600 ppt (isoprene-d2) was achieved. Simultaneous monitoring of both compounds allowed the detection of labelling levels down to 6% (isoprene-d2 in total isoprene) with a time resolution of 3 min.