Thousands of animals, many of them endangered, are part of the count which is required by law as part of the zoo's licence.
Important details about each and every individual are noted down so that the zoo can help worldwide breeding programmes.
Newsround's Martin headed to the zoo, which houses over 400 different species, to find out how it's done.

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Will your choices see you matched to Lennox Lewis, do your picks make you a modern day Rocky Marciano, or perhaps you'll come out as the greatest of all time - Muhammad Ali.
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The rig ran aground off Lewis during a storm on Monday while being transported to Malta.
Sightseers have been warned to stay away from the scene of the grounding, and a 300m temporary exclusion zone has been put in place around Dalmore beach.
The Maritime and Coastguard Agency said it was necessary to keep roads clear.
The rig, which is carrying 280 tonnes of diesel oil, broke free from its tug during towing and severe weather prevented the line being reconnected.
A salvage team began an inspection of the structure on Tuesday in preparation for the more detailed assessment.
Hugh Shaw, the Secretary of State's Representative for Maritime Salvage and Intervention, said the initial survey was to check "a number of things including fuel tanks".
Officials said the aim was to carry-out as much work as possible on Wednesday while the weather was favourable, but warned that work to refloat the rig could take some time.
Mark Rodaway, of the Maritime and Coastguard Agency, said it was necessary to keep roads clear for emergency crews and salvage teams.
He said: "We understand that this incident is of interest to people living in the area but we're asking them to stay away to ensure easy access for emergency services and salvage teams.
"Also the last thing we want is for people to be injured or worse trying to get a closer look on remote cliff paths."
Three vessels including the emergency towing vessel Herakles are the scene of the grounding.
Union Bear, a multipurpose offshore vessel, has also arrived at Stornoway Harbour from Aberdeen to assist in the salvage operation.
There were no personnel aboard the 17,000-tonne drilling rig when it became detached from the tug in the early hours of Monday, 8 August.
The semi-submersible platform was being towed from Norway to Malta from where,  it is understood. it was to be taken to Turkey to be scrapped.
The Marine Accident Investigation Branch has begun an inquiry into what happened
Keepers at Chester Zoo are making sure every creature, from the biggest elephant to the smallest beetle, is present and correct as part of their annual animal count.
[NEXT_CONCEPT]
Are you all-out aggression, do you outsmart your opponents, or do you win through sheer willpower?
[NEXT_CONCEPT]
Salvage teams working at the Transocean Winner oil rig are expected to carry out a detailed inspection later on Wednesday.