The stable carbon isotope ratio (δ13C) values of sedimentary long chain (> C20) n-alkanoic acids from the equatorial Pacific (IODP Sites U1331–1338) were measured for historical reconstruction of C4 plant contribution from South America over the last 40 Ma. The values for C30 and C32 acids ranged between −36.9‰ and −25.4‰, suggesting that they likely originated from higher plant wax associated with C3-dominated vegetation. The molecular distribution of alkanoic acids in the sediments showed a marked change across the Intertropical Convergence Zone (ITCZ), indicating a potential contribution from the Northern Hemisphere to the sediments located at > 10°N. In contrast, the abundances of n-alkanoic acids significantly decreased in the sediments at < 10°N. The results suggest that the ITCZ may have acted as an effective barrier for the atmospheric transport of terrigenous biomarkers from the Northern Hemisphere, and the records presumably reflect the plant wax signal from the northern part of South America. The latitudinal variation in the δ13C values suggest that the differences in the core locations possibly caused north- and southward shifts of ca. −1.0‰/°N and ca. +0.5‰/°S from the equator, respectively. The corrected δ13C values of C30 and C32 acids did not cross the C3 end member threshold until 1.7 Ma, despite the onset of C4 plants in central South America at ca. 7 Ma. This implies that vegetation in the low latitudes of South America was less affected by hydrological changes induced by the uplift of the Andes during the late Miocene.