The Spanish researchers will attempt to characterise the bacterial strains in two different types of the cheese. They will then monitor the products throughout the ripening process to understand how the micro-organisms interact and change.
The study, run by the Department of Microbiology at the University of Granada, hopes to learn more about what influences the taste and feel of the cheeses. It also aims to dispel safety fears about Andalusian goat's cheese, which is made from raw milk.
The debate over the safety of raw, or unpasteurised, milk in dairy products is ongoing.
Several states in the US have banned the practice, while Britain's Food Standards Agency warns on its website that "young children, elderly people, pregnant women and people who are ill should avoid unpasteurised milk".
The Andalusian study team said that uncovering the genetic identity of Andalusian goat's cheese could help to show consumers it is safe, and so help producers commercialise the product.
They are particularly keen to understand the role of the enterococci bacteria in the cheese.
The bacteria, found in the human intestine, is usually associated with faecal contamination of food. The researchers said, however, they believed the bacteria was not harmful and may even help to fight off pathogens. It is also thought the bacteria often isolates itself from traditionally-produced cheeses.
"Even in industrially-produced products we have found enterococci, and it does not mean that they are unfit," said professor Manuel Martínez Bueno, the project leader.
Andalusian goat's cheese, considered a local speciality and often preserved in olive oil, has fallen on hard times recently alongside other parts of the dairy industry in the region.
The University of Granada said the area's cattle sector had shrunk by half in the last 30 years.