The team says it found a particular DNA signature which recently appeared in Lebanon and is probably linked to the crusades.
The finding comes from the Genographic Project, a major effort to track human migrations through DNA.
Details of the research have been published in the American Journal of Human Genetics.
The researchers found that some Christian men in Lebanon carry a DNA signature hailing from Western Europe.
Four crusades came through Lebanon between the 11th and 13th Centuries - the first, second, third and sixth. The bulk of the crusader armies came from England, France, Germany and Italy; many of the men stayed to build castles and settlements, mixing with the local populations.
The scientists also found that Lebanese Muslim men were more likely than Christians to carry a particular genetic signature. But this one is linked to expansions from the Arabian Peninsula which brought Islam to the area in the 7th and 8th Centuries.
But they emphasise that the differences between the two communities are minor, and that Christians and Muslim Arabs in Lebanon overwhelmingly share a common heritage.
The legacy of the Muslim expansion has been demonstrated in other studies which looked at the genetics of Middle Eastern and North African populations. But signs of recent European migration to the region are more unusual.
The study focused on the Y, or male, chromosome, a package of genetic material carried only by men that is passed down from father to son more or less unchanged, just like a surname.
The goal of the study was to put some science to the history of this country
Pierre Zalloua, Lebanese American University
These can be used to classify male chromosomes into different groups (called haplogroups) which, to some extent, reflect a person's geographical ancestry.
The team analysed the Y chromosomes of 926 Lebanese males and found that patterns of male genetic variation in Lebanon fell more along religious lines than along geographical lines.
A genetic signature on the male chromosome called WES1, which is usually only found in west European populations, was found among the Lebanese men included in the study.
Science and history
"It seems to have come in from Europe and is found mostly in the Christian population," said Dr Spencer Wells, director of the Genographic Project.
"This is odd because typically we don't see this sort of stratification by religion when we are looking at the relative proportions of these lineages - and particularly immigration events."
He told BBC News: "Looking at the same data set, we saw a similar enrichment of lineages coming in from the Arabian Peninsula in the Muslim population which we didn't see [as often] in the Christian population."
Lebanese Muslim men were found to have high frequencies of a Y chromosome grouping known as J1. This is typical of populations originating from the Arabian Peninsula, who were involved in the Muslim expansion.
"The goal of the study was to put some science to the history of this country - which is very rich," said Pierre Zalloua, a co-author on the paper, from the Lebanese American University in Beirut.
He added: "To have these great civilisations - with the Islamic expansion and the migration from Europe - coming to Lebanon, leaving not only their genes but also some of their culture and way of life, it can only make us feel richer."
The Genographic Project was launched by National Geographic in 2005 to help piece together a picture of how the Earth was populated.
The consortium has sold 250,000 DNA test kits and regional centres have taken samples of genetic material from 31,000 indigeous people.