[7] Although several zoos and wildlife associations have instituted programs for the iguanas on Utila, the species still finds itself threatened due to overhunting and may face more of a threat in the form of habitat loss.

[4] Endemic to Utila, an island off the northern Honduras coast, Ctenosaura bakeri is an inhabitant of 8 square kilometres (3.1 sq mi) of mangrove forests.

[1] Unique among iguanids and rare among reptiles, it is believed that C. bakeri was pushed into the mangrove swamps due to competition from the larger, more aggressive C. similis, which typically inhabits the drier habitats on Utila.

[5][10] From evolutionary and ecological perspectives, inhabiting brackish mangrove forests entails very specific adaptations of diet, behavior, and resource utilization.

[6] Adults make their homes within holes in various mangrove trees and maintain an arboreal existence whereas the young are strictly terrestrial for the first year of their lives.

[7] As a result, the Iguana Research and Breeding Station was built in April 1997 with the help and funds of various organizations such as the Frankfurt Zoological Society, the Senckenberg Nature Research Society, AFE-COHDEFOR (State Forestry Administration-Honduran Forestry Development Corporation), BICA (Bay Islands Conservation Association) and the National Autonomous University of Honduras.

[11] This species currently has an estimated wild population of 10,000 animals in 2–3 subpopulations, but is greatly threatened by loss of habitat,[7] as mangrove forests are being used as garbage dump sites and deforested for the construction of homes, resorts, and marinas.

According to a survey conducted by the IUCN, exotic invasive plants cover the ground near the mangroves and make the area inappropriate for nesting sites.

[8][12] In 2004, as a result of Köhler's expedition and subsequent book, Reptiles of Central America, the Conservation Project of the Utila Iguana (CPUI) was founded.

In September, 2007, the London Zoo successfully managed to breed Ctenosaura bakeri for the first time outside of Utila, an important step to ensure their survival if the species is lost from its natural habitat by hurricanes or over-hunting.