DNA analyses performed on the human skeletal remains document the presence of mitochondrial haplogroup D which occurs widely in the Americas.

[4] After the discovery of animal bones in 1994, Timothy H. Heaton, paleontologist with the University of South Dakota-Vermillion at the time, led the research project, assisted in 1996 and after by Fred Grady with the Smithsonian Institution.

[2][5] A tribal group in the area of the discovery, the Tlingit, submitted DNA samples to be compared to the On Your Knees Cave individual.

[9] This, given On Your Knees Cave's location on an island, suggests a maritime adaptation was present at an early time level in this region.

The evidence from this site suggesting a marine based diet, extralocal artifacts, and a maritime adaptation supports a coastal migration model for the first Americans as proposed by K.R.

[12][disputed – discuss] In accordance with the Native American Graves Protection and Repatriation Act of 1990, excavations at On Your Knees Cave were halted after the discovery of human skeletal remains in 1996.

[4] After the discovery, Heaton and other project leaders contacted and began consulting with local tribal governments in the area to determine the ownership of the remains.

The Tlingit had their reservations about allowing scientists to test the remains, but finally agreed to analyses of the human bones and further excavation[4] if they were notified of any additional discoveries.