Self-assembled monolayer (SAM) formation of alkanethiols with ionic, hydrophilic terminal functionalities onto various O-2 plasma/ethanol pretreated gold substrates was characterized to explore the effect of gold surface oxide on the SAM packing quality. Oxygen adsorption induced by the Au2O3 surface residuals are observed on the plasma-oxidized and O-2 plasma/ethanol-rinsed pretreated Au surfaces while no obvious adsorbed oxygen is found on freshly coated and O-2 plasma/ethanol sonication pretreated Au substrates. A model for the formation of hydrophilic terminated SAMs, -OH, -COOH, and -PO3H2 is proposed. According to this model, the ionic and/or other binding interactions between the surface Au2O3 and the alkanethiol hydrophilic terminal end as well as the interactions between the terminal SAM functionalities could cause the packing disorder found on these three SAMs formed on Au substrates containing Au2O3 surface species.