The skeletal evidence for early modern human occupation of South Asia is sparse. Sri Lanka has been occupied by modern humans from the terminal Pleistocene, with a skeletal record indicating continuity of occupation and settlement into the late Holocene. This study focuses on the analysis of fragmented human remains dated to the mid-Holocene recovered from a salvage archaeology operation conducted at a shell midden in the coastal village of Mini-athiliya in southern Sri Lanka. The Mini-athiliya site has been radiocarbon dated to ca. 3600 b.p. Large quantities of estuarine, marine, and terrestrial shells, stone tools, lithic debris, and animal bones were associated with the human skeletal remains recovered from this shell midden. The skeletal remains, faunal remains, and stone tools from this site have been greatly disturbed by recent shell mining activities. Much of the material collected from the piles of debris was mixed, fragmented, and out of context.Our study refers to associations we make to the cultural assemblage from this site to make inferences on the context of skeletal remains found. The minimum number of individuals (MNI) identified from commingled remains is five. In addition, another individual from an undisturbed context from this site was previously reported. Based on tooth eruption and the presence and level of dental attrition, the estimated age at death for these individuals ranges from 5 to 45 years. Heavy attrition in the adult dentition indicates a highly abrasive diet with a marked absence of caries among these relatively robust people. This study contributes to the understanding of the bioarchaeological aspects of mid-Holocene aquatic foragers who were contemporaries of early agricultural people of South Asia, while describing a framework for managing a skeletal sample from a disturbed context.