The process of fuel-air mixing in the Direct Injection Spark Ignition (DISI) engine is highly unsteady and three-dimensional with wide cycle-to-cycle variations involving vaporization of droplets and its interaction with large-scale turbulent flow field. Although the majority of the past numerical studies of mixing in an Internal Combustion (IC) engines have employed Reynolds-Averaged Navier-Stokes (RANS) equations with empirical turbulence model, here we have implemented a Large-Eddy Simulations (LES) with the Linear-Eddy Model (LEM) for subgrid scalar mixing into a commercial IC engine simulation code (KIVA-3V). This study shows that when time-accurate effects are included significantly different results are obtained. These differences between the original KTVA-3V and the new KIVALES in predicting the in-cylinder turbulent fuel-air mixing are discussed. LES shows highly unsteady, anisotropic in-cylinder fuel-air mixing process compared to the original KIVA-3V. The implications for combustion is also discussed.