He argued that man was descended from apes, and natural selection was the means by which some species prospered while others failed.
But he could give no explanation on how species originated, and only now is there overwhelming fossil evidence of the transitional forms his theory clearly called for.
His opponents, primarily Creationists, claim his theories are totally incompatible with a religious vision of reality. They believe that man was formed in the image of God.
Sky News has been under a strict embargo not to reveal details of Ida's discovery, and so has been unable to contact religious groups for reaction to the news.
But in the face of what scientists say is a hugely-convincing body of evidence, will the fighting over Darwin's legacy continue? And if so, for how long?
This year, the Vatican admitted that Darwin's theory should not have been dismissed and says it is compatible with the Christian view of Creation.
Marking the 150th anniversary of Darwin's On the Origin of Species, it said that while the Church had been hostile in the past to his work, the idea of evolution could be traced hundreds of years further back to St Augustine and St Thomas Aquinas.
The 4th century theologian St Augustine had never heard the term evolution, but knew forms of life transformed over time. And Aquinas made similar remarks in the Middle Ages.
The Roman Catholic Church has also been playing down the idea of Intelligent Design, which argues a "higher power" must be responsible for the complexities of life.
To mark the bicentenary of Darwin's birth, the Church of England also sought to bring Darwin back into the fold with a page on its website paying tribute to his work.
It highlighted his strong connection with the Church and how he had trained as a clergyman before losing his faith "by a need for evidence, and the sad death of a beloved daughter", and then had been inspired to go into science by a fellow cleric.
In its centre-piece essay, the Darwin tribute concluded that a healthy balance between the mystery of faith and the wonders of scientific discovery is essential.
"There is no reason to doubt that Christ still draws people towards truth through the work of scientists as well as others, and many scientists are motivated in their work by a perception of the deep beauty of the created world," it said.
But the Church could not resist a health warning, and warned of the "social misapplication of Darwin's discoveries, where natural selection justifies racism and other forms of discrimination".
Young Earth creationists though are likely to be skeptical about the importance of Ida's discovery, and what scientists say is proof of a missing link between man and the animal kingdom.
They believe the Earth, the heavens and life itself were created by God between 6,000 and 10,000 years ago.
One of the groups, America's Christian Reformed Church, believes: "Humanity is created in the image of God; all theorising that minimises this fact, and all theories of evolution that deny the creative activity of God are rejected.
"The clear teaching of Scripture and the confessions rules out holding views that support the reality of evolutionary forebears of the human race. But further investigation or discussion regarding the origin of humanity should not be limited."
It will be interesting to see theology's view of the transitional species Darwin always dreamed existed, but never got to see. +++++++++++++++++++++++++++++++++++++++++++++++++++
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