Two 400-year-old skeletons were uncovered during restoration work on St Tugual's Chapel in Herm.
The discovery was made while a soak away was being dug to collect run off rainwater on the Manor House lawn, to the south of the chapel.
The skeletons of an adult and a child have been estimated to be between 400 and 500 years old.
They were removed for examination on Friday and experts are expected to excavate three further part skeletons.
Andrew Bailey, the island's finance director, said: "It was a bit of a surprise. "It's not every day you dig up your back lawn and find a few remains in there.
"We had long suspected there would be remains in that area given the proximity to the chapel, but no one had ever found any.
"We have no records at all so we're really hoping the archaeologists can give us some information about the remains they have found, it would be interesting to fit them into the Herm timeline."
As to the possible identities of the skeletons he said: "At that time it was largely the preserve of monastic orders so monks and farmers were around at that point."
Tanya Walls, secretary of the Archaeology Section of La Societe Guernesiaise, said: "Clearly this is a cemetery with several burials and the bones are well preserved.
"We don't think they're very, very old as in medieval but perhaps in the latter part of the medieval period maybe 400, 500 years ago.
"The only way to date the burials definitely is to have it scientifically done by radio carbon dating and that's quite an expensive process and very specialised.
"It means small samples of bone have to sent over to the UK, so that's something we'll look into doing and we'll have to see if it's possible or not.
"What we're going on is our knowledge of the condition of the bone that is found the island."
She said finding the bones just 2ft (60cm) deep was not surprising.
"It's only in the last couple of hundred years perhaps that people have had an idea that's it's important to bury people deeply from a health point of view," she said.
"It could indicate that they didn't have a lot of time and there have been suggestions that maybe there could have been some disease or something like that and they were burying quite a few people."
Ms Walls added that further research would be carried out on the skeletons.