The researchers propose that the effect is due to molecules in the seminal fluid of the first mate being absorbed by the female's immature eggs and then influencing the growth of offspring of a subsequent mate.
This confronting idea, known as telegony, dates back to ancient Greek times, but was discredited in the early 20th Century with the advent of genetics.
To test it out, University of New South Wales (UNSW) Australia scientists manipulated the size of male flies and studied their offspring.
"Our discovery complicates our entire view of how variation is transmitted across generations, but also opens up exciting new possibilities and avenues of research. Just as we think we have things figured out, nature throws us a curve ball and shows us how much we still have to learn," said lead author Dr Angela Crean.
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The team produced large and small male flies by feeding them diets as larvae that were high or low in nutrients. They then mated the immature females with either a large or a small male.
"We found that even though the second male sired the offspring, offspring size was determined by what the mother's previous mating partner ate as a maggot," said Crean.
Despite major advances in genetics, many questions remain about how some traits are inherited, researchers said.
"We know that features that run in families are not just influenced by the genes that are passed down from parents to their children. Various non-genetic inheritance mechanisms make it possible for maternal or paternal environmental factors to influence characteristics of a child," said Crean.
"Our new findings take this to a whole new level - showing a male can also transmit some of his acquired features to offspring sired by other males. But we don't know yet whether this applies to other species," she said.
The idea of telegony - that a male can leave a mark on his mate's body that influences her offspring to a different male - originated with the Greek philosopher Aristotle.
It was a concern to royalty in the 1300s and still popular as a scientific hypothesis in the 1800s but rejected in the early 1900s as incompatible with the new science of genetics, researchers said.