In the 1990s, subgenus Chelonoidis was elevated to generic status based on phylogenetic evidence which grouped the South American members of Geochelone into an independent clade (branch of the tree of life).

The subspecies inhabiting Floreana Island (C. niger)[36] is thought to have been hunted to extinction by 1850,[37][38] only 15 years after Charles Darwin's landmark visit of 1835, when he saw shells, but no live tortoises there.

[39] However, recent DNA testing shows that an intermixed, non-native population currently existing on the island of Isabela is of genetic resemblance to the subspecies native to Floreana, suggesting that C. niger has not gone entirely extinct.

[68] Hope was bolstered by the discovery of a C. n. abingdonii hybrid male in the Volcán Wolf population on northern Isabela, raising the possibility that more undiscovered living Pinta descendants exist.

[76] By classifying the Cerro Fatal tortoises into a new taxon, greater attention can be paid to protecting its habitat, according to Adalgisa Caccone, who is a member of the team making this classification.

Only the longevity of giant tortoises allowed them to survive until the Galápagos National Park, Island Conservation, Charles Darwin Foundation, the Raptor Center, and Bell Laboratories removed invasive rats in 2012.

[81] In 2019, an elderly female specimen was finally discovered on Fernandina and transferred to a breeding center, and trace evidence found on the expedition indicates that more individuals likely exist in the wild.

[43] The extinct Santa Fe subspecies has not yet been described and thus has no binomial name, having been identified from the limited evidence of bone fragments (but no shells, the most durable part) of 14 individuals, old eggs, and old dung found on the island in 1905–06.

When a saddleback tortoise withdraws its head and forelimbs into its shell, a large unprotected gap remains over the neck, evidence of the lack of predation during the evolution of this structure.

In combination with proportionally longer necks and limbs,[25] the unusual saddleback carapace structure is thought to be an adaptation to increase vertical reach, which enables the tortoise to browse tall vegetation such as the Opuntia (prickly pear) cactus that grows in arid environments.

[95] The shell distortion and elongation of the limbs and neck in saddlebacks is probably an evolutionary compromise between the need for a small body size in dry conditions and a high vertical reach for dominance displays.

[99] They have been documented feeding on Hippomane mancinella (poison apple), the endemic guava Psidium galapageium, the water fern Azolla microphylla, bromeliad Tillandsia insularis and the Galápagos tomato Solanum cheesmaniae.

[100] Juvenile tortoises eat an average of 16.7% of their own body weight in dry matter per day, with a digestive efficiency roughly equal to that of hindgut-fermenting herbivorous mammals such as horses and rhinos.

I was always amused, when overtaking one of these great monsters as it was quietly pacing along, to see how suddenly, the instant I passed, it would draw in its head and legs, and uttering a deep hiss fall to the ground with a heavy sound, as if struck dead.

[49] When mature males meet in the mating season, they face each other in a ritualised dominance display, rise up on their legs, and stretch up their necks with their mouths gaping open.

[49] This is one of the few vocalisations the tortoise makes; other noises are made during aggressive encounters, when struggling to right themselves, and hissing as they withdraw into their shells due to the forceful expulsion of air.

[49] It is carried out blindly using only the hind legs to dig a 30 cm (12 in)-deep cylindrical hole, in which the tortoise then lays up to 16 spherical, hard-shelled eggs ranging from 82 to 157 grams (2.9 to 5.5 oz) in mass,[41] and the size of a billiard ball.

I never dreamed that islands, about fifty or sixty miles apart, and most of them in sight of each other, formed of precisely the same rocks, placed under a quite similar climate, rising to a nearly equal height, would have been differently tenanted.

[121] It has been suggested[122] that this oversight was made because Darwin only reported seeing tortoises on San Cristóbal[123] (C. chathamensis) and Santiago[124] (C. darwini), both of which have an intermediate type of shell shape and are not particularly morphologically distinct from each other.

[128] Darwin later compared the different tortoise forms with those of mockingbirds, in the first[129] tentative statement linking his observations from the Galapagos with the possibility of subspecies transmuting: When I recollect the fact that [from] the form of the body, shape of scales and general size, the Spaniards can at once pronounce from which island any tortoise may have been brought; when I see these islands in sight of each other and possessed of but a scanty stock of animals, tenanted by these birds, but slightly differing in structure and filling the same place in nature; I must suspect they are only varieties ...

[86] Several waves of human exploitation of the tortoises as a food source caused a decline in the total wild population from around 250,000[111] when first discovered in the 16th century to a low of 3,060 individuals in a 1974 census.

Another subspecies, C. n. abingdonii, became extinct on 24 June 2012 with the death in captivity of the last remaining specimen, a male named Lonesome George, the world's "rarest living creature".

"[138] In the 17th century, pirates started to use the Galápagos Islands as a base for resupply, restocking on food and water, and repairing vessels before attacking Spanish colonies on the South American mainland.

[42] Feral pigs, dogs, cats, and black rats have become predators of eggs and young tortoises, whilst goats, donkeys, and cattle compete for grazing and trample nest sites.

The extinction of the Floreana subspecies in the mid-19th century has been attributed to the combined pressures of hunting for the penal colony on the relatively small island, the conversion of the grazing highlands into land for farming and fruit plantations, and the introduction of feral mammals.

The Galápagos giant tortoise is now strictly protected and is listed on Appendix I of the Convention on International Trade in Endangered subspecies of Wild Fauna and Flora (CITES).

Eggs are collected from threatened nesting sites, and the hatched young are given a head start by being kept in captivity for four to five years to reach a size with a much better chance of survival to adulthood, before release onto their native ranges.

[17] The 15 remaining tortoises were brought to the Charles Darwin Research Station in 1971 for a captive breeding program[156] and, in the following 33 years, they gave rise to over 1,200 progeny which were released onto their home island and have since begun to reproduce naturally.

The tortoises are a keystone species, acting as ecosystem engineers[161] which help in plant seed dispersal and trampling down brush and thinning the understory of vegetation (allowing light to penetrate and germination to occur).

Its goal is to assist the Galapagos National Park to effectively conserve giant tortoises by conducting cutting-edge applied science, and developing an inspirational tortoise-based outreach and education programme.