The team, based at France's National Institute of Agronomic Research (INRA), said they had mapped out the gene sequence for one of the two bacterial strains present in yoghurt - Lactobacillus bulgaricus.
The breakthrough is a major step in understanding the of make-up of yoghurt, thought to be more than 5,000 years old. The other bacteria present - Streptococcus thermophilus - was also mapped out recently.
The success should eventually make it easier for dairy firms looking to create more added value and functional yoghurt products. Yoghurt drinks, and probiotic ones in particular, have increasingly led dairy market growth in recent years thanks to consumer health trends.
"We now have knowledge that was not there before," said Emmanuelle Maguin, a member of the INRA team, to DairyReporter.com.
"A few years ago, this was not very well explored. When we started we only knew about 30 genes in the bacteria, but now we have the complete genome sequence." There are around 1,800 genes in Lactobacillus bulgaricus.
Maguin said the research had enabled the team to understand more about which genes performed certain functions, and how the bacteria could evolve and change in yoghurt.
She said this could help both scientists and dairy firms research more efficiently by taking some of the trial and error out of testing different product formulations.
"Before, I had to see what worked and what didn't work, but that's all changed now. We can now see the different cells and understand more about what they do."
There is more work to be done, however, and the INRA researchers now plan to examine more closely how the two bacteria in yoghurt interact, particularly during the fermentation process.
French dairy group Danone, which owns the popular probiotic brands Activia and Actimel, has helped to fund two of the scientists working on INRA's yoghurt genome project.
Danone has been involved in several research projects in this area, and last autumn told DairyReporter.com it hoped to develop several new strains of probiotic bacteria in the next few years.