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Self-assembled monolayers (SAMs) of terphenylthiol (TP0) prepared on Au(111) from ethanolic solution at room temperature and subsequently annealed at different temperatures of up to 473 K were investigated using scanning tunneling microscopy and infrared reflection absorption spectroscopy. Upon annealing, the TP0 adlayer formed a series of different structural phases with different molecular arrangements. Our results show that SAMs prepared at RT without annealing and SAMs annealed at 313 K exhibited the formation of a closely packed “α” structure where TP0 molecular axes are orientated almost upright. The formation of the α-phase was accompanied by the formation of a loosely packed phase (β-phase). During annealing from 333 to 473 K, the results revealed the formation of different structural phases, namely, γ, δ, ε, σ, and ϕ. With the exception of the ϕ-phase, the phases were found to form loosely packed structures with the molecular axes largely tilted away from surface normal but do not form “flat-lying” phases. Surprisingly, upon annealing at 453 K, the SAMs exhibited a phase transition to a higher dense network of molecular structure (ϕ-phase) with almost upright standing molecules. An additional annealing at 463 K led to a significant increase in the size of the well-ordered domains of the ϕ-phase at the expense of their density. At the same time, a partial desorption of the TP0-SAMs was noticed to take place. The formation of a densely packed phase upon annealing and subsequently desorption of TP0 molecules from this state completely contradicts the behavior of n-alkanethiol and other oligophenylthiol SAMs, in which desorption occurs from lying-flat geometry. The ϕ-phase, which was the only one remaining on the surface, did not cover more than 30% of the gold surface area. A further increase of the annealing temperature to 473 K caused a substantial increase in the number of the desorbed molecules. Therefore, a remarkable reduction in both the size and density of the ordered domains of the ϕ-phase was observed. On the other hand, the annealing temperature was found to have a significant influence on both the appearance and the shape of the gold islands. Moreover, it has been found that the gold islands, regardless of their shapes, were always covered by standing-up, densely packed, and ordered phases such as the α- and ϕ-phases.