Like all Bahamian rock iguanas, this species is protected in the Bahamas under the Wild Animals Protection Act of 1968. It is listed in Appendix I of the CITES convention. Allen's Cay was formerly over-run by the common house mouse (Mus musculus), an invasive species, and these were in their turn attracting barn owls (Tyto alba) from neighbouring islands. In May 2012, Island Conservation and the Bahamas National Trust worked together to remove invasive house mice from Allen's Cay to protect the Audubon's shearwater and hopefully also native species such as the Allen Cay rock iguana and the Bahama yellowthroat. As it was feared the Allen Cay rock iguana might eat the rodenticide used to rid the island of the mice, eighteen were transplanted to nearby Flat Rock Reef Cay, where another small population already existed. Sixteen of these had starved to death by 2013. It is now thought this was because the plants on Flat Rock Reef Cay lacked the extra nutrients found on Allen's Cay. After this at least eight iguanas survived on Allen's Cay, and including the two from Flat Rock Reef Cay, there are now ten iguanas thought to be left on the island. In 2012, Iverson had begun a project to fill a small sinkholes on the island with sand to create suitable breeding ground.
