The data set contains branched and isoprenoid GDGT data from modern surface soils and soil profiles across transects in tropical South America. The data covers all major vegetation types including the Atlantic rainforest, the Amazon rainforest, Cerrado types of different density, the Caatinga shrublands and grasslands and riparian forests from the Llanos. The goal of the data collection was to test the impact of the different vegetation types on both branched and isoprenoid GDGT distributions. Measurements were conducted with a HPLC/APCI-MS system on lipid extracts that were further separated into different fractions using column chromatography prior to analysis.