Careful quality control of complex matrices such as fuels and food is necessary due to the prevalence of counterfeit and pirated goods in global trade. The addition of taggants (indicator substances) to products or their packaging helps to ensure traceability. In order to prevent the mixing of different liquid products, such as different taxed fuels, invisible labelling (marker) can be used to detect illegal activities. This study investigates the qualitative and quantitative analysis of markers in complex fuel matrices using Resonance-Enhanced Multiphoton Ionisation (REMPI) Ion Mobility Spectrometry (IMS). The potential of REMPI as a selective ionisation technique for the detection of markers is highlighted, particularly with respect to minimizing matrix background and the possibility of detection without chromatographic pre-separation. Finding a suitable marker-wavelength combination that provides a suitable marker-to-matrix ratio allows selective ionization of markers while minimising matrix background. Matrix analysis shows that higher excitation wavelengths result in reduced matrix signals, with the low intensities observed at 355 nm for diesel and petrol matrices. Several candidate markers are evaluated based on the criteria of intense signal at 355 nm and non-leachability for the low tax labelling. The analytical performance of selected markers is evaluated, with a focus on the charge transfer reaction (CTR) between markers and matrix components. Our findings demonstrate the potential of REMPI-IMS for marker analysis in fuels without the need for chromatographic pre-separation, providing a promising approach for detecting illegal or fraudulent activities in the supply chain.