Incest
The key theme of the book is incest; Eugenia is having an affair with her brother, Edgar, who is a sexual deviant, and his actions do support her protestations that she tried to break off the affair but he would not allow her to do so. The affair has been going on since both siblings were children, and it is the most passionate and deep relationship that Eugenia has in her life. It is also something that she is willing to sacrifice the lives of others over; for example, her former fiance killed himself after finding out about the affair.
The incestuous affair affects William deeply, not, perhaps, in such an emotional way as it did his predecessor in her life, but in his relationship with his children, who, he comes to realize, are not actually his children at all, but Edgar's. He also realizes that Eugenia only married him so that she could present a facade of propriety to society whilst hiding the incestuous relationship going on behind closed doors.
Sexual Abuse
Edgar is in love with his sister and has been having a sexual relationship with her since they were both barely more than children. However, he is also an insatiable sexual deviant and a rapist. William discovers this for himself when accidentally finding Edgar raping an under-age teen servant in the stables one afternoon, and when he confronts his brother-in-law about it, is roundly threatened. The girl, of course, frightened of losing her job, agrees with Edgar's assertion that the sex is consensual (although this does not really address the problem of her being under sixteen.)
Victorian Prurience and Propriety
In Victorian England, appearances were everything. It didn't matter what was going on behind closed doors as long as nobody could see it. Outward appearances were all that mattered, and this was a particularly starchy period in the nation's history. Edgar, deviant and involved in a sexual relationship with his own sister, is seen as far more palatable by well-to-do society than is William, because William, whilst a man of great academic talent, has no money and no social position. This, Edgar believes, makes him wholly unsuitable as a husband for his sister. Matty, the Alabaster family tutor, also feels constrained by her reliance on such a debauched family for her income. However, to the outside world, both Eugenia and Edgar as seen as the type of person everyone should aspire to be.
An Era of Discovery
Despite the heavy overtones of Colonialism in Victorian England, there was also an exciting "off shoot" of this, with far less political intent. This was a time of discovery, of adventure, of striking out to as yet unchartered waters of the globe. This was particularly true in the areas of science, anthropology, and botany. William has travelled extensively and has just returned from a study field trip along the Amazon. He is writing a book about what he has seen and found there. He is also working on a second book; Matty, too, has ambitions to travel and see the world. This is the first generation to whom travel was possible outside of governmental or military purposes. It is a time of excitement and anticipation, where academia blends with general interest, and to the Victorians, the possibilities seemed limitless.
Love
Despite the book's emphasis on sexual perversity at the expense of love, there is also the smallest element of a love story within it. Matty, the put-upon governess at the Alabaster home, falls quickly in love with William. For his part, he greatly enjoys her company, and feels a strong bond with her, although as a married man he puts any other feelings about her to the side. Matty purchases two tickets for a trip along the Amazon, one for her, one for him. Although he is reluctant to go at first, William finally admits that he loves Matty, as she does him. At the end of the book, despite the pain and unpleasantness it has taken them to get there, the two protagonists are able to finally admit that they have fallen in love.
Chauvinism and the Beginning of Suffrage
Matty purchases two tickets for the Amazon, intending to take the trip herself even if William decides not to go with her. This is the time of early feminism, and of suffrage, when it finally dawned on women that unless they wanted to be chained to the kitchen in perpetuity, they had better strike out and do something for themselves. Meek, mannerly Matty is one of these women. However, William, for all his attributes, is not exactly a feminist. He immediately says no to the trip, not because he doesn't want to take a trip with Matty but because he believes the Amazon is no place for a woman. This demonstrates the way in which women were still looked at as delicate little things, when in fact, women like Matty were taking steps to prove that they are exactly the opposite.
