The bird was traditionally known locally as the solan goose, and its eggs and meat were considered delicacies.
It is estimated that in 1850 almost 2000 birds were harvested from the rock.
The rabbits were bred for food but they were wiped out by myxomatosis in the 1950s.
They have also been affected by the successive influences of Celtic, Norse and English-speaking peoples during the historic period and this is reflected in their names.
The islands also came under attack from Vikings during the early Historic period.
There are signs that the puffins are starting to return to the island to breed.
Several of the islands contain pre-historic remains created by cultures whose names are unknown.
The Firth is an important area for nature conservation and has a range of habitats including extensive mudflats, shingle shorelines and saltmarsh.
The last named, which is well developed on Alloa Inch, is typically dominated by saltmarsh rush, sea club-rush, sea aster and common saltmarsh-grass.
The Earl of Somerset garrisoned the islands in 1547 after the Battle of Pinkie Cleugh.
His force of marines were ordered to reinforce Inchkeith, and they built a large square fort, with corner towers, on the site of the present day lighthouse.
There are few islands off eastern Scotland and most of any size are in this group.