A team of Australian scientists has made a major breakthrough in mapping the koala genome and stopping the spread of chlamydia that is crippling koala populations.

After just six months, the scientists have come more than half way to mapping the genome, identifying 12,000 of the koala's 20,000 genes.

By mapping the entire genome they eventually hope to develop a vaccine to fight diseases like chlamydia.

Professor Peter Timms from the Queensland University of Technology is part of the research team.

"We're able to now really accelerate our progress towards understanding why some different strains of chlamydia affect koalas and how we can make a vaccine that hopefully will go a long way towards immunising both captive koalas and also in the wild," he said.

Chlamydia causes infertility and blindness and has wiped out koala populations in New South Wales and Queensland.

But Professor Timms says the scientists are trying to establish why populations in Victoria remain virtually unaffected.

"We know that koalas are infected with various strains of chlamydia, but we do not know why some animals go on to get severe clinical disease and some do not," he said.

Dr Rebecca Johnson from the Australian Museum says they have also discovered that koalas share similarities with the Tasmanian devil.

"There are some really interesting comparisons," she said.

"We will be able to fit it into other animals like the Tasmanian devil that is known to suffer from very low population diversity and significant or serious diseases and we hope that there will be some outcomes there."

Koalas are now considered threatened under national law.