The mammal, previously only seen in small numbers in northern Germany, was found in the Blackdown Hills on the border of Devon and Somerset.
Britain has only one native species of dormouse - which has hazel fur. The black colour is thought to be caused by a recessive gene.
The animal was discovered in a nest box used to monitor the species, which is threatened with extinction in the UK.
More on the black dormouse, plus more Devon and Cornwall news
Claire Groom from the Blackdown Hills Area of Outstanding Natural Beauty said: "This is the very first time a black dormouse has been recorded in the UK.
"The black colouration is likely to be due to a recessive gene, so rather than being a new species it is probably an interesting and extremely unusual quirk of nature."
It is believed the black dormouse was born in the UK and a sample of its fur has been taken for DNA analysis.
Five black dormice were seen in Germany in 1972 and, after many years of searching, two more were discovered last month.
They were found in a nest containing a normal golden-coloured mother, with four juveniles, two of them hazel coloured and two of them black with a white throat - identical to the Devon specimen.
Britain's native dormouse has declined by more than a third since the year 2000, wildlife charity the People's Trust for Endangered Species said last month. A report showed that hazel dormice are extinct in 17 English counties.
Ian White from The People's Trust for Endangered Species said: "The National Dormouse Monitoring Programme has been running for more than 25 years, with volunteers collecting data on thousands of dormice.
"Not once has anyone come across a black dormouse."
A black dormouse has been discovered in the UK for the first time.