The genes mainly affect the width and 'pointiness' of noses which vary greatly between different populations, said researchers from University College London (UCL).
The new information adds to our understanding of how the human face evolved and may help contribute to forensic DNA technologies that build visual profiles based on an individual's genetic makeup, they said.
Researchers identified five genes which play a role in controlling the shape of specific facial features. DCHS2, RUNX2, GLI3 and PAX1 affect the width and pointiness of the nose and another gene - EDAR - affects chin protrusion.
"It brings us closer to understanding how genes influence the way we look, which is important for forensics applications," he added.
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People have different shaped facial features based on their genetic heritage and this is partly due to how the environment influenced the evolution of the human genome.
The nose, for example, is important for regulating the temperature and humidity of the air we breathe in so developed different shapes in warmer and cooler climates, researchers said.
"Identifying genes affecting nose shape provides us with new tools to examine this question, as well as the evolution of the face in other species," said Ruiz-Linares.
"It may also help us understand what goes wrong in genetic disorders involving facial abnormalities," he added.
Researchers collected and analysed DNA samples from 6,630 volunteers in Brazil, Colombia, Chile, Mexico and Peru.
After an initial screen, a sample size of 5,958 was used. This group included individuals of mixed European (50 per cent), Native American (45 per cent) and African (5 per cent) ancestry, resulting in a large variation in facial features.
A subgroup of 3,000 individuals had their features assessed using a three-dimensional reconstruction of the face in order to obtain exact measurements of facial features and the results identified the same genes, researchers said.
The study identified genes that are involved in bone and cartilage growth and the development of the face, they said.
The findings were published in the journal Nature Communications.