The characters in The Alleys of Eden struggle with issues of personal identity and sociocultural identity. Each struggles to define the self, grappling with the complexities of language, culture and political ideology. Neither main character wishes to engage in the struggle. Simply keeping a sense of self while relating to the beloved other requires more effort and understanding than either can consistently muster.

Past actions shape the present and future.

What are the costs to an individual of belonging to another person in a love relationship? What are the costs to an individual of belonging to a social group? When is a homeland not a homeland? For Butler's protagonists in this novel, external forces pressure the individuals to choose sides when they never really wanted to do so. Languages, customs, laws and combat all force Cliff and Lanh to choices they would rather avoid.