We investigated branched and isoprenoid glycerol dialkyl glycerol tetraethers (GDGTs) in surface soils and a paleosol sequence to understand the effects of environmental and postdepositional factors on branched GDGT composition in different soil types and to reconstruct the past changes in the mean annual air temperature (MAAT) in southwestern Japan during the last 15 ka. The estimated MAAT was overestimated by 6 degrees C and 2 degrees C when the global and regional soil calibrations were applied, respectively. Additionally, the estimated MAAT increased downward by a maximum of 4 degrees C in the upper 30 cm of the soil sequence. This is likely to reflect the addition of newly produced branched GDGTs in subsurface soils. The estimated MAATs in a paleosol sequence are thus similar to 10 degrees C and similar to 6 degrees C higher than those expected when the global and regional soil calibrations were applied, respectively, but the variation agrees with the Holocene variation in the MAAT estimated by the pollen assemblage. This indicates that the MBT'/CBT-derived MAAT is biased, but the variation reflects the past changes in MAAT.