One of the novel's themes is the vast difference in mindset and sensibility between town and country dwellers. In his natural urban environment, Sherlock Holmes is able to draw upon his remarkable capacity for rational thought in arriving at his unerringly accurate deductions. Out in rural areas, however, he finds his rational methodology challenged by the assumptions, prejudices, and superstitions tenaciously held by country folk. Somehow Holmes must remain true to his principles while all around him people are proposing all manner of superstitions and legends to account for all the grisly goings-on out on the moor.

The thematic conflict between town and country finds its clearest expression in the person of Dr. Watson, whose contempt for country folk and their superstitions is downright scathing. Dismissing the natives as little more than primitives Watson treats Devonshire as if it were a distant civilization, rather than a part of his own country.

Indeed, the general portrayal of country life in the story is not portrayed by subtle means. One gets the impression that Conan Doyle may have partly chosen to set The Hound of the Baskervilles in the country in order to give Holmes the opportunity to demonstrate the superiority of rationalism over superstition in solving seemingly insoluble mysteries.

One theme in The Hound of the Baskervilles is the way in which preconceptions and prejudices lead people astray. When Dr. Mortimer first tells Sherlock Holmes about Sir Charles Baskerville's death, Dr. Mortimer includes a long-winded and far-fetched tale about an ancient hound who plagues many generations of the Baskerville family. Dr. Mortimer believes this hound was to blame for Sir Charles's sudden demise. The dog is essentially what's called, in mystery parlance, a red herring, or a clue that is meant to set the reader and the detective on the wrong path in solving the mystery. Another red herring in the book is Selden, the mysterious convict on the moors, as well as Barrymore the butler, who is acting strange but really is just providing food to Selden, his wife's brother. The real murderer, Stapleton, appears innocuous until later in the book, but the reader might be thrown off at first by preconceptions about an escaped convict or about a mysterious hound. Holmes, on the other hand, is not led astray by preconceptions.

Another theme is the wildness of the moors, far from the civilizing effect of London. It is on the moors that the apparent demon hound runs wild, and the escaped convict, Selden, also roams on the moors. People believe Baskerville Hall is haunted by the demon dog, and the moors are a place where the supernatural and the Gothic loom large. 

An important Hound of the Baskervilles theme is the primacy of reason and rationalism. People are manipulated and exploited through their superstitious beliefs—such as a belief in a supernatural hound. Holmes is at pains to show that the answer to any mystery is grounded in empiricism, not fairy stories. He methodically uses logic to unravel a problem and is never satisfied with weak or irrational explanations.

Another theme is the exploitation of women through the pretense of love. Evil men manipulate the love of the women in their lives to gain help or to cover up illegal acts. For instance, Selden takes advantage of  his sister's love for him to aid him in evading justice. Stapleton is not above using his own wife to help destroy Sir Henry Baskerville. Stapleton also feigns love for Laura Lyons in order to persuade her to lure Sir Charles down a dark corridor. This novel shows us that to abuse love is to show an evil nature. 

"Avarice is the root of all evil" is another theme: the desire for the Baskerville estate leads Stapleton to murder. 

Theme is the guiding message of the story.  In The Hound of the Baskervilles, the themes can best be described as

• What goes around comes around
• Greed is a powerful motivator
• Appearances can be deceiving
• We cannot be ruled by our fears

The first theme is evident in that Hugo Baskerville who tried to lock up the dame and then chase her down with a hound.  As a result, he died a violent death.  This was not because of a curse, but because of the natural consequences of his violent and impulsive actions.  This also results in his family’s reputation being tarnished by the curse.  The same theme follows Stapleton, because his harsh behavior was his doom.

Greed is a strong presence in the book.  It was what caused the original Baskerville to lock the young lady up and what led Stapleton to charade around as a simple naturalist.  The absence of greed in Sir Henry Baskerville, Holmes, and Watson is a great contrast.

Almost no one and nothing is what it seems in this book.  From the hound to the convict, things and people are revealed throughout the story as different from what is expected.  The same is true of Holmes, since he is supposed to be in London but is really hiding on the moor.  The supposedly harmless Barrymores are harboring a convict, and Stapleton is not only the murder, but his sister is really his wife.

Sir Charles Baskerville is so focused on his fear of death and the hound that he allows his judgment to be impaired.  At times, Watson and Sir Henry are also afraid, but they survive because they keep their wits about them and refuse to succumb to fear.