The genes were found on chromosomes six and nine
Scientists say they have begun to crack the genetic code that helps determine when a girl becomes a woman.
A UK-led team located two genes on chromosomes six and nine that appear to strongly influence the age at which menstruation starts.
The Nature Genetics study also provides a clue for why girls who are shorter and fatter tend to get their periods months earlier than classmates.
The genes sit right next to DNA controlling height and weight.
The two to three-year transition from childhood to adult body size and sexual maturity
Complex multi-staged process involving growth acceleration, weight gain and the appearance of secondary sexual characteristics
Can happen earlier in overweight and obese chidlren
Early puberty associated with increased risk for obesity, diabetes and cancer
A second paper, published in the same journal, also concludes that one of the two genes highlighted by the first study plays a key role in the timing of puberty in both girls and boys.
Reproductive lifespan is closely linked to the risk of developing conditions such as heart disease, breast cancer and osteoporosis.
It is thought that the female sex hormone oestrogen - produced at higher rates during a woman's reproductive life - raises the risk of these diseases.
Therefore, the earlier a woman goes through puberty, the more risk she may be at.
So the researchers say their work not only improves our understanding of the genetics underpinning development, it may ultimately aid the fight against disease.
However, they also accept that the onset of puberty is influenced by factors such as nutrition and exercise, and the effect of a single gene is likely to be relatively small.
In the western world children are reaching puberty at younger and younger ages - some girls at the age of seven.
Many blame rising obesity rates because, generally, girls who achieve menstruation earlier in life tend to have greater body mass index (BMI) and a higher ratio of fat compared to those who begin menstruation later.
From its analysis, a team led by Exeter's Peninsula Medical School predict one in 20 females carry two copies of each of the gene variations which result in menstruation starting earlier - approximately four and half months earlier than those with no copies of the gene variants.
In collaboration with research institutions across Europe and the US, they studied 17,510 women from across the world, including women of European descent who reported reaching menstruation of between nine and 17 years of age.
When they split the women up according to the age they began menstruating, certain gene patterns appeared.
Scanning the whole genome enabled them to hone in on these differences and pinpoint the exact genes most likely accountable.
Researcher Dr Anna Murray said: "This study provides the first evidence that common genetic variants influence the time at which women reach sexual maturation.
"Our findings also indicate a genetic basis for the associations between early menstruation and both height and BMI."
Co-worker John Perry said: "Understanding the biological mechanisms behind reproductive lifespan may also help inform us about associated diseases that affect a lot of women as they get older, including diabetes, heart disease and breast cancer."
The second paper, led by the MRC Epidemiology Unit at Cambridge, analysed genetic information from thousands of people.
It linked a specific variant one of the two genes highlighted by the Exeter team - LIN28B - with earlier breast development in girls, and earlier voice breaking and pubic hair development in boys.
Lead researcher Dr Ken Ong said: "LIN28B works by controlling whether or not other genes are active.
"There are a number of such 'master switch' genes known, but this is the first evidence linking such a gene to growth and physical maturation."
Dr Aric Sigman, psychologist and fellow of the Royal Society of Medicine, said: "Early menstruation is a health issue because beyond being an inconvenient surprise for a girl and her parents, it's also associated with a higher risk of a variety of diseases and psychological problems.
"Girls maturing earlier are more likely to become depressed, delinquent, aggressive, socially withdrawn, suffer sleep problems drinking, smoking, drug abuse, lower self-esteem and suicide attempts.
"They're also more likely to exhibit poor academic performance in high school than on-time or later maturing peers.
"It is important that we understand why early menstruation occurs and these findings bring us closer to explaining this in some girls."
Three other papers, also published in Nature Genetics, throw up other candidate genes which appear to be involved in the onset of puberty.