The book, initially valued between £15,000 and £25,000, was sold from Lady Mary Stewart's library at Lyon & Turnbull's Edinburgh auction rooms.
The book, published in 1859, is a work of scientific literature which is considered to be the foundation of evolutionary biology.
As Lady Mary Stewart explained in a letter to a London bookseller, her great grandfather sailed on board The Beagle, leading her to add one of the most sought-after works of natural history to her library.
Darwin was born in Shrewsbury in 1809 and spent much of his early life in the town. He is regarded as the town's most famous son and in 2009 activities were held to mark the 200th anniversary of his birth.
Simon Vickers, head of the rare books and manuscripts department at Lyon & Turnbull, said:
"The book is probably the most important biological breakthrough in the 19th century.
"It has affected the study of biology and is a very important textbook. It is one of the most important scientific books written ever.
"We sold a copy about five years ago that made £12,000 but this one has been repaired and rebacked and is in good condition."
The book was among 450 lots at Wednesday's auction and generated a lot of interest from bidders online, on the phone and on the auction floor.
As a well-known author of romantic novels, Lady Stewart's most famous novels included the Arthurian trilogy: The Crystal Cave, 1970, The Hollow Hills, 1973 and The Last Enchantment, 1979.
Mr Vickers added: "Lady Mary Stewart not only had a passion for writing books, but also collecting them.
"Indeed, there is scarcely an area of human endeavour that has not been impacted by Darwin's theory, the terms Darwinism and Darwinian now being integral parts of the modern lexicon.
"Lady Mary Stewart also developed an interest in the illustrated, deluxe edition works of Arthur Rackham, Edmund Dulac and Kay Nielsen. Each purchase was made in careful consultation with London booksellers, who would especially look out impressive copies of these coveted works, which reflect her interest in the myths and legends of the past."