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This paper highlights the value of pollen-analytical studies in the prehistoric archaeological context at the Fa Hien rock shelter. The Fa Hien rock shelter located in the Wet Zone of southwestern Sri Lanka has been occupied by the earliest anatomically modern humans in South Asia, dating from the late Pleistocene to the middle Holocene. The pollen evidence from the samples associated with the early Holocene human skeleton from this site has been used to assess the burial context and palynological taphonomy. Pollen data analysis indicates that high taphonomic impact occurred on the pollen grains in the depositional context, possibly due to reworking, burning, mechanical pressure and other possible human and animal activities. Furthermore, the pollen assemblage appears to have been primarily derived from the lowland rainforest, including disturbed habitats. Along with archaeological stratigraphy and radiometric dating, the pollen assemblage can be used to make broad inferences on the burial contexts and environment of the rock shelter occupants, while discussing the significance of forensic palynology in the Fa Hien archaeological context.