Founded in 1996 by two former National Marine Fisheries Service (NMFS) scientists, Bill Gilmartin and Hannah Bernard, the organization is a 501(c)(3) nonprofit dedicated to the conservation of Hawai'i's native wildlife through research and education. Gilmartin and Bernard, both award-winning marine biologists and conservationists, are also members of government-appointed advisory boards dealing with Hawai'i marine and terrestrial issues. These boards and committees include: Society for Marine Mammalogy, the Hawaiian Monk Seal Recovery Team, Pacific Scientific Review Group, Offshore Cetacean Take Reduction Team and the Hawai'i County Public Access, Open Space and Natural Resources Preservation Commission.

The critically endangered status of the Hawaiian monk seal initially drew the two together to form HWF to support NMFS in this species' recovery. Gilmartin's work with monk seals as the leader of the NMFS Protected Species Investigation Program in the Northwestern Hawaiian Islands was featured in the January 1992 issue of National Geographic. Bernard's work on Hawaiian monk seals on Maui was featured in the December 2005 issue of Coastal Living magazine.

HWF has focused on recovery actions for the endangered hawksbill sea turtle in Hawai'i including nest protection and identifying foraging habitat and prey species. HWF has supported outreach education on marine life conservation through naturalist training programs and student projects.

Cheryl King joined HWF in 2000 and manages HWF's hawksbill sea turtle program on Maui. She also works for the Kahoolawe Island Reserve Commission.

Recently, HWF has been involved in marine debris recovery efforts in the NWHI and the South Point (Ka Lae) area of Hawai'i Island directing a community effort in pulling nearly 100 tons of marine debris from the coast there. On that same shoreline, HWF is working with the State of Hawaii to manage the recovery and protection of native plants and anchialine pools in a recently designated coastal “forest reserve.”