A proper methodological approach of investigating Holocene sea level changes is a prerequisite in order that the sea-level index points can be useful and significant. This requires the correct identification of the indicative meaning. The indicative meaning of the sea level indicator is defined as the altitudinal relationship of the local environment in which it accumulated to the contemporaneous reference tide level. This study identifies the index points using the litho-, bio-, and chrono-stratigraphic approach. The sea level indicator is derived from the regressive contact of the intercalated peat and marine clastic sequence, while the indicative meaning is estimated based upon the relationship with the contemporary samples. The study was carried out at two contrasting coastal locations, the fossil sites from Meru and Mardi in Kelang in the west and Penur (north and south transects) in Kuantan in the east, while the contemporary sites are from various ecological environments from both areas. Microfossil analysis of pollen and diatoms indicates that the former are more applicable, and defined the changing microfossil assemblages within the regressive contact of the sea level indicator samples. Seven sea level index points are identified. The finding agrees to the general assumptions of high mid-Holocene sea level history in peninsular Malaysia. A relative sea level difference between the west and east coast is indicated, but the significance, if any, is dealt with caution. The explanations of presumed differential crustal movement or sheer age/altitude variability of the index points are suggested.