Women who were on average heavily overweight in the year following childbirth had the 825T gene, a German study found.
Those who did not have it returned to their normal weight after giving birth without the need for rigorous exercise.
The scientists, writing in the Lancet medical journal, described 825T as a "thrifty gene" which boosts the body's ability to store fat, particularly when it is scarce.
Of two pregnant women with the same food intake, the one with the gene would put on more weight, said Professor Winfried Siffert.
He said a third of white European women have the gene, with the proportion rising to eight-in-ten among Aborigines.
Seriously overweight
Being seriously overweight carries an increased risk of diabetes and heart disease.
But Professor Siffert said that exercise was effective in losing weight for women with the gene.
He added: "Being a carrier might have been advantageous in hunter-gatherer societies, in that prevention of post-pregnancy weight loss increased the breast feeding capability of the mother."
In a separate article in the Lancet, researcher Berthold Hocher and colleagues from the Humboldt University of Berlin, Germany, linked the same gene in mothers to low birthweight of their babies.
He said: "Given that birthweight is a multifactorial phenomenon, involving factors such as non-genetic socio-economic circumstances, as well as maternal and foetal gene alterations, the association of the 825T allele is striking."
An allele is a series of two or more different genes that occupy the same position on a chromosome.
Rosie Dodds, policy research officer for the National Childbirth Trust, said the finding that a gene was responsible for weight retention after birth "made sense".
She added: "There are some women who find it much more difficult to lose weight after they have a baby.
"In terms of significance to women, it doesn't alter what they do or the information we give because you don't know what your gene structure is."
Strict diets were to be discouraged after birth, particularly if the woman was breast feeding, she said. Getting exercise from brisk walking or swimming could be beneficial.
The trust provides information leaflets on safe eating and exercise for women who have given birth.