Lady Audley's Secret plays on Victorian anxieties about the domestic sphere. The home was supposed to be a refuge from the dangers of the outside world, but in the novel, the seemingly perfect domestic lady turns out to be a violent criminal who has not only tried to commit murder but who has also committed bigamy and abandoned her child. This unsettled Victorian readers because it indicated that the concepts of "the perfect lady/mother" and "domestic bliss" were more idealistic than realistic. In addition, anxieties about the increasing urbanisation of Britain abound; the city gives Lady Audley the power to change her identity because it renders its citizens effectively anonymous. The small town of Audley is no longer a refuge where everyone knows the life story of every neighbour; the residents of Audley must accept Lucy Graham's account of herself since they have no other information about her past. Other anxieties about unstable identity appear throughout the novel: Robert's relationship with George has homosexual overtones, especially considered in light of his attraction to Clara, George's sister, who is described as looking identical to George. Additionally, Lady Audley's maid, Phoebe, resembles Lady Audley, thus banishing the idea of physical distinction between the upper and lower classes and therefore of any inherent superiority of the former.
Lady Audley's Secret is, furthermore, a story about gender and class, and Lady Audley's objectionable upward mobility suggests a threat to the paradigm of social class. Madness is also a key issue. Lady Audley and others often converse about the meaning of this word, but many readers believe that Lady Audley is not mad. In fact, many critics view Lady Audley's deception as a feminist act in which a woman takes control of the direction of her own life.
The novel mirrors many of the same themes from the real-life Constance Kent case of June 1860 that gripped the nation with headline news for years. The first instalment of Lady Audley's Secret came out almost exactly one year after the Kent murder. The novel, like the real-life case, featured a wicked stepmother (and former governess who married a gentleman), a mysterious and brutal murder in a country manor house, a body thrown down a well, and characters fascinated by madness. Constance Kent can be seen in many of the female characters in the novel: the murderess Lady Audley, the tomboyish Alicia Audley, the restrained Phoebe Marks and the lonely Clara Talboys. Jack Whicher, the detective and case investigator, can be seen in the character of Robert Audley.