The Western Foothills of Taiwan was known to be composed of Late Oligocene to Pleistocene shallow marine strata continuously deposited on the stable passive Chinese continental margin without significant stratigraphic break. Here we present multiple micropaleontological evidences, including occurrence of larger foraminifera Discocyclina dispansa ex. interc. sella-dispansa and calcareous nannoplanktons, to show that there are Middle Eocene marine strata (first named as the Chungliao Formation) exposed in the Tsukeng anticline of the Western Foothills, central Taiwan. Occurrences of intact tests with thin delicate outer rims and well-preserved embryonic chambers suggest that the Discocyclina dispansa ex. interc. sella-dispansa (Lutetian to Bartonian in the Tethys region) are buried indigenously on shallow inner shelf during an episodic transgression in the Early Middle Eocene. The conclusion is consistent with a biostratigraphy study of calcareous nannoplanktons (Zones NP14–15) in the shale/sandstone alternations overlying the Discocyclina-bearing bed of the Chungliao Formation and calcareous nannofossils of Zone NP16 integrated with an age dating of 38.8±1Ma (Late Middle Eocene) on zircon grains of the overlying Pinglin Tuff. The Middle Eocene syn-rift sequences (Chungliao Formation and Pinglin Tuff) exposed along the Tsukeng anticline are unconformably covered by the latest Oligocene–Miocene post-rift sequence, a scenario similar to what have been drilled in the East China Sea-Taiwan Strait-South China Sea. This rift basin (named as the Nantou Basin) is sitting on the Peikang Basement High margin which further extends southwestward to the Central Uplift of the Pearl River Mouth Basin in the northern slope of the South China Sea. The present work documents a hitherto unknown occurrence of the exposed early Tertiary marine rift basin sequence in the Western Foothills of Taiwan. The study extends our knowledge of the Western Foothills geohistory from the Late Oligocene downward to the Early Middle Eocene. The occurrence of the Paleogene Nantou rift basin in the Western Foothills may also suggest that there could have similar Paleogene rift sequences exposed in other parts of the Taiwan mountain belt like the Hsüehshan Range and the Central Range east of the Western Foothills.