The blaze, which was described by emergency services as a 'major incident' who sent 75 firefighters to tackle it, started at around 11.30am.
The flames killed a number of breeds, including question mark cockroaches, Amano shrimps, betta hendra fish, cinnamon frogs, tentacled snakes, and grosbeak starlings.
In an official statement, Chester Zoo Chief Operating Officer Jamie Christon described Saturday as 'one of the toughest days' in Chester Zoo's history.
"All of our mammal species - such as critically endangered Sumatran orangutans, Sulawesi macaques, endangered silvery gibbons and even birds such as rhinoceros hornbills were led to safety by our conservationists in partnership with the emergency services," he added.
"However, now that our teams have started to assess the site, we are devastated to confirm the small number of species that we were unable to save. These include a number of question mark cockroaches, Amano shrimps, betta hendra fish, cinnamon frogs, tentacled snakes and birds such as grosbeak starlings."
He said new homes have been found within the zoo for all of the animals who were saved from the blaze.
This isn't the first time Chester Zoo has made headlines in recent months; in October two baby elephants died.
Nandita Hi Way, three, and Aayu Hi Way, 18-months-old, were struck by a virus, leaving staff reportedly fighting to save the animals.
The deaths left campaigners asking questions about whether the animals belonged in zoos, with the Born Free Foundation saying: "Born Free is convinced that life in zoos greatly compromises elephant welfare and does little or nothing to assist in the protection of elephant populations where they belong - in the wild."