The composition of fuel blends containing up to 20% of fatty acid methyl esters has been determined using a Shimadzu heart-cut chromatographic system with a GCMS-QP2010 Ultra mass-spectrometric detector and a quadrupole mass filter. Commercial diesel has been used as hydrocarbon fuel. The analysis of fuel blends has shown that heart-cut two-dimensional gas chromatography with mass spectrometric detection allows successful determination of fatty acid methyl esters in the hydrocarbon fuel with different relative amounts of the esters. The procedure developed has been also tested for tackling the problem of identification of fuel type in a model spill on water surface and the time since the spill.