In 1998 there were only 30-40 red squirrels remaining on Anglesey. These formed a single isolated population in the eastern part of Pentraeth forest.
A comparative analysis of hair samples taken from the forest population and material collected from island specimens living within broadleaved woodland sites on Anglesey twenty years ago showed that the island has lost much of the genetic diversity which was once present. By the late 1990s only a single haplotype (in simple terms one female bloodline) remained and was shared by all the animals in the Pentraeth forest population.
Download the B BC News Report on Welsh red squirrel genetics
Download the Conservation Genetics Paper (2005)
This historical research also revealed that there were several red squirrel bloodlines that were unique Wales. These genetic types have, to date, not been found anywhere else in the UK, but in 2011, studies revealed that an animal imported from the European mainland had a similar bloodline.
The red squirrel population on Anglesey has been bolstered with a series of reintroductions. Hair samples were collected from many animals that were used in the release program and genetic profiles were created. These studies revealed that the reintroduction projects involved a genetically rich and diverse range of animals.
In 2010, the Wildgenes Lab at Edinburgh Zoo screened hair samples collected from 100 red squirrel samples that were collected from sites across the island. In the single largest red squirrel genetic study in the UK patterns of gene flow on the island were revealed.
The key findings were:
1. That there had been an increase in the genetic variation on Anglesey.
2. That the number of bloodliines had risen from one to six since 2002/3.
3. That animals had dispersed into Pentraeth forest from adjacent reintroduction sites.
4. That Newborough forest contained the largest single red squirrel population and that genetic types not reintroduced there had arrived through red squirrel dispersal.
5. It was recommended that additional hair sampling takes place and to that end in 2011 and 2012 the Trust aim to collect 200 red squirrel hair samples.

In 2010 and 2011 the Trust also collected 50 grey squirrel hair samples from Anglesey and the Gwynedd mainland. These, along with an archive of 60 hair samples collected from the island in 2007, will allow researchers in London to measure the genetic diversity in the grey squirrel populations in this part of the North Wales coast and to gauge how isolated Anglesey is from the mainland populations.