They found evidence that married couples are more likely to have genetic differences in a DNA region governing the immune system than were randomly matched pairs.
This was likely to be an evolutionary strategy to ensure healthy reproduction because genetic variability is an advantage for offspring, Maria da Graca Bicalho and her colleagues at the University of Parana in Brazil reported.
"Although it may be tempting to think that humans choose their partners because of their similarities, our research has shown clearly that it is differences that make for successful reproduction, and that the subconscious drive to have healthy children is important when choosing a mate," Bicalho said in a statement.
Scientists said it was not clear what signals attract the body to people who are genetically dissimilar to themselves, but suggested body odor or even face structure could play a role.
Bicalho said the team compared genetic data from 90 married couples with data from 152 randomly generated control couples.
They found the real couples had significantly more dissimilarities in MHC.
"Parents with dissimilar (genetic regions) could provide their offspring with a better chance to ward infections off because their immune system genes are more diverse," they wrote in a summary.
Previous studies have suggested animals may use body odor as a guide to identify possible mates as being genetically similar or dissimilar, she added, but other physical factors may also be involved.
"Other cues such as face symmetry might play a role as well, but they are still in the field of speculation," she said.