In a previous study, in order to investigate the effect of charge stratification on combustion behavior such as combustion efficiency and combustion phasing which also largely affects the emissions, an experiment was conducted in a heavy-duty compression ignition (CI) metal engine. The engine behavior and emission characteristics were studied in the transition from HCCI mode to PPC mode by varying the start of injection (SOI) timing. To gain more detailed information of the mixing process, in-cylinder laser diagnostic measurements, namely fuel-tracer planar laser induced fluorescence (PLIF) imaging, were conducted in an optical version of the heavy-duty CI engine mentioned above. To the authors’ best knowledge, this is the first time to perform fuel-tracer PLIF measurements in an optical engine with a close to production bowl in piston combustion chamber, under transition conditions from HCCI to PPC mode. Results show that four mixing schemes can be distinguished as the SOI timings are varied during the transition. They are linked to the results presented in the reference paper, where emissions were varied in different zones. For SOI at -100 crank angle degree (CAD), fuel distribution is homogeneous as expected. With other SOI timings, a significant part of the fuel mixture was trapped in the squish region and crevice area before start of combustion (SOC) as shown by PLIF results. The observations in the reference metal engine paper were confirmed by this measurement. Results are also in good agreement with computational fluid dynamics (CFD) simulations performed for this engine.