It is very problematic to suggest that a work of literature has but one theme, as the very nature of literature is to open itself to a wide variety of different meanings that can be read into it through the reader and the reader's own understanding and context.
However, having said this, one of the major themes is the treatment of women in this novel and the various ways in which they are supressed, abused and mistreated. Afghanistan under the Taliban is shown to be a patriarchal world taken to its logical and terrifying extreme, with women forced to wear burkas and having no choice in whom they marry and no rights whatsoever. This is of course why Laila suffers so greatly because she was raised by her father to believe in herself and have a voice. The reality of her life with Rasheed is thus incredibly difficult for her. This is also why there was never any hope of justice for Mariam for her murder of Rasheed. Men were considered superior to women in any matter of law or justice.
Linked to this theme is the way that women are shown to live their lives in fear. The various examples of violence against women, both in the domestic sphere and in the wider sphere, reinforce the powerless position that women occupied and the way in which they could be abused at any moment with no hope of justice or salvation.