Black Turtle Cove. Image: Alamy

Black Turtle Cove is a labyrinth of salt-water inlets and home to three kinds of mangrove: black, red and white, named not after any obvious colouration but after their distinctive leaves and roots. As we were punted along, we spotted rays flapping their wings near the surface some were huge mantas, but others were covered in bright golden dots. Hernn said these were spotted eagle rays, smaller but if anything more beautiful. The surface went quiet for a moment, while I watched a lava heron hop from branch to branch, seeming to follow our zigzagging through the channels. A small bird a mangrove finch, I think was tailing the heron. I asked Hernn if this was some obscure act of symbiosis, and he said he didnt know. I found this comforting; the Galapagos should harbour mysteries.

Then someone spotted a shadow in the water. We all leaned over, looking out for rays again or, alerted by the guide, for small sharks which sometimes hunt in the mangrove. What we saw, however, were green sea turtles giant, peaceful beauties, rising to the surface to peer at us with one eye and take in some air before gently slipping back under the water.

One of the islands most iconic species, the sea turtle is an antidote to anxiety (even on a cruise, that most relaxed of pursuits, there is plenty of anxiety about as wildlife-watchers stress out with their cameras and competitive natures). At Punta Vicente Roca , I got to swim beside green turtles, their calm movement and manners seeming to belong perfectly in the silent chamber of the sea. I dived to watch them nibble on the moss-like algae that grows on coral and rocks, using flippers to propel themselves with surprising nimbleness through the currents and crevasses.

A giant tortoise at the Charles Darwin Research Station. Image: Alamy

If anything, the land tortoise is more talismanic still. At Puerto Ayora on Santa Cruz Island , we disembarked to visit the Charles Darwin Research Station and see one of the two main towns of the Galapagos. This, as it happened, was just a few days before the death of Lonesome George, the most famous of the islands giant tortoises. The last of the Pinta Island subspecies , he was living with two females, Georgina and Georgette, at the time. Biologists were hoping he would get inspired, breed with these younger girls and provide us with some living genes but it was not to be. George did a lot to put the Galapagos on the map, but his most important legacy is the breeding centre at the research station, where hundreds of tortoises of every age and size munch away safely in their pens.

Puerto Ayora was also a bridge into a different reality. A cruise ship never feels quite normal, somehow the lavish food, the lazy rhythms, the Jacuzzi and the exam-free lectures but when you walk along the front at Puerto Ayora , you are back in Latin America. Its a pretty place, with that breezy air of a small coastal town, and it was lovely to stay on land while my fellow passengers returned to the Eclipse for lunch. My girlfriend and I shared a pizza and a cold beer, then strolled to the fish market where a land iguana was fighting with a pelican over a huge fish bone and a cheeky lava gull was stealing bass steaks.

With that kind of little drama unfolding in town, you could be forgiven for becoming a little blas in the Galapagos. Some species are extremely common (or at least commonly seen), such as blue-footed boobies , pelicans, Sally Lightfoot crabs and yet another species named after the volcanic soil the lava lizard. But the islands remain a fragile environment. After

one evening lecture, I asked Mark Carwardine how the islands were doing and what challenges they faced. People, he said, meaning both the number of people visiting and the number of people living there to support tourism. The government doesnt even know how much water the islands have, Carwardine added, or how much they need.

The impact of your own presence, lets face it is apparent as soon as you step off the boat. From Puerto Ayora, we travelled inland to visit a tortoise reserve and en route saw shoddy buildings and a swathe of forest being cleared for a large estate. In conservation terms, Carwardine explained, the Galapagos are a qualified success. The main endemic species have been protected, theres a cap on the number of visitors [150,000 per annum] and the authortities are trying to eradicate introduced species, in particular dogs. But there is still a lot to do. The key thing is to use tourism to pay for the conservation projects; people used to talk about completely closing the islands, but they do have to pay for themselves.

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The Galapogos Islands: animal magic