The evolution means the insects could become immune to strategies adopted to control malaria which kills thousands of people around the world, especially in Asian and African countries.
Researchers at the Imperial College London who studied Anopheles gambiae mosquito, chiefly responsible for spreading malaria in sub-Saharan Africa, found that two strains of the mosquito were rapidly diverging in their genetic make-up, despite appearing physically identical.
Dr Maria Lawniczak, a member in the research team, said: "From our new studies, we can see that mosquitoes are evolving more quickly than we thought and that unfortunately, strategies that might work against one strain of mosquito might not be effective against another."
"It's important to identify and monitor these hidden genetic changes in mosquitoes if we are to succeed in bringing malaria under control by targeting mosquitoes," Dr Lawniczak was quoted as saying by the Daily Mail.
According to the scientists, genetic differences between the two strains, known as M and S, were scattered throughout the insects' DNA. The changes had occurred in areas likely to affect development, feeding behaviour, and reproduction, they said.
A further study comparing the two strains showed they seemed to be evolving differently.
This was thought to be in response to different environmental factors such as larval habitats, infectious agents and predators.
Co-author Professor George Christophides, also from Imperial College, said: "Malaria is a deadly disease that affects millions of people across the world and amongst children in Africa, it causes one in every five deaths.
"We know that the best way to reduce the number of people who contract malaria is to control the mosquitoes that carry the disease.
"Our studies help us to understand the makeup of the mosquitoes that transmit malaria, so that we can find new ways of preventing them from infecting people."
The scientists detailed their findings in the journal Science.