Located about six miles from the town of Friendship in Muscongus Bay, this 12-acre island supports nesting gulls, eiders, black-crowned night herons, Leach's storm petrels, and ospreys. The island is partially covered by red spruce with abundant raspberry thickets, grasses, and forbs. Franklin Island was listed on the State Register of Critical Areas in October, 1977 for its unique value to nesting eiders. At one time, the eider nesting density was the highest in the state with over 1,400 nests packed into six acres. Fewer eiders nest there today, mainly due to an outbreak of cholera that hit the area in the 1980's. The U.S. Coast Guard transferred the island to the U.S. Fish and Wildlife Service in 1973 and still maintains the historic light house on the island.

The U.S. Government acquired Franklin Island in 1806 and completed construction of the lighthouse in 1808. This was the third lighthouse built in Maine, and the U.S. Coast Guard continued to staff the lighthouse for 160 years before the station was automated in 1967. The U.S. Fish and Wildlife Service acquired Franklin Island in 1973, making this the first island acquired for the Petit Manan National Wildlife Refuge Complex.

Franklin Island once supported one of the largest common eider colonies in Maine. Unfortunately, the eider colony was decimated by avian cholera in the mid 1980's. The population has slowly recovered, and a 2003 survey documented over 330 pairs of eiders and over 100 pairs of great black-backed and herring gulls.