Ionic liquids (ILs) exhibit a unique nanoscale structure (i.e., nanodomains) characterized by their organization into distinct domains. We present evidence of nanodomains in trihexyl(tetradecyl)phosphonium chloride, [P66614][Cl], using single-molecule tracking (SMT) and the maximum entropy method (MEM) to analyze single-molecule trajectories. The diffusion properties of ATTO 647N were assessed as the temperature of [P66614][Cl] increased from 20 °C (4020 cP), 35 °C (1239 cP), 45 °C (599 cP) to 50 °C (439 cP). The MEM analysis revealed a distinct two-population distribution of diffusion coefficients representing nanodomains in [P66614][Cl] at 20 °C (4020 cP). The slow population accounts for 16%, with a diffusion coefficient of 0.104 μm2/s, while the fast population constitutes 84% with a diffusion coefficient of 0.634 μm2/s. Two diffusing populations were also measured for the chemically different probes ATTO 647N, DiD, and Nile Blue chloride in [P66614][Cl] at 20 °C. In contrast, only a single fast population was measured in [P66614][Cl] at 50 °C. At a similar viscosity (640 cP) but a lower temperature of 20 °C, trihexyl(tetradecyl)phosphonium bis[(trifluoromethyl)-sulfonyl]imide, [P66614][NTf2], also showed only a single diffusing population. The elimination of the slow population and the presence of a single diffusing population in [P66614][Cl] as the temperature increases and the viscosity decreases is consistent with liquid-liquid phase separation (LLPS) as a mechanism of nanodomain formation. In addition, the measurement of two diffusing populations for three fluorophores with different chemical structures is also consistent with a physical mechanism, and not a chemical mechanism, for nanodomain formation.