Temporal stability of close- packed thiophene ( TP) self- assembled monolayers ( SAMs) on Au( 111) was investigated by scanning tunneling microscopy ( STM). Molecular- scale STM imaging reveals that the structural transitions of TP SAMs in the structure and size of ordered domains and the distribution of vacancy islands ( VIs) occurs after long- term storage for 1 year. During this time period, the ordered domain sizes were remarkably increased and the fraction of the areas of the VIs to the total surface area was steeply decreased from 6.5% to 1.7%. We demonstrate that the temporal factor strongly affects two- dimensional SAM structures and our results will be very useful in designing a molecular template for SAM- based further applications.