The mother-daughter relationship drives the plot in Annie John and is its primary theme. The difficulties and tensions in this relationship stem from Annie's inability to accept the fact that she is a separate self. Kincaid paints Annie's desire to remain united with her mother as an emotion shared by most girls of her age. Annie's classmates all commiserate with her essay about her fear of separation. Furthermore, the girls befriend one another in an effort to find substitutes for the maternal love that appears to be dissipating. As Annie ages, she finds herself caught between love and hatred for her mother, which drives her to be both a good student and a disobedient child. Again, the rationale behind her adolescent rebellion seems to be proffered as an explanation for a general psychological trend rather than merely a specific fictional phenomenon. The dynamics of mother-daughter relationships take up a prominent place in Jamaica Kincaid's work and have frequently appeared in her other novels such as Lucy and The Autobiography of My Mother.
Antigua was colonized by the British until 1967 and remained a commonwealth in 1981. As Annie John takes place in the 1950s, it remains in the colonial period. Kincaid explores the colonial relationship particularly through her discussion of the school that Annie attends. It is run as a British institution and all the materials taught in the school deal with English literature, history, and culture. The girls dress in a formal British style and they are discouraged from engaging in local activities, such as calypso dancing in the playground. Annie's musing on the failure of the school to discuss the negative history of slavery and her delight in the imprisonment of Columbus highlight the ways in which the school teaches the students not to question the history and social order that is being handed down to them. Annie excels in her school, which shows that she has learned all of the skills necessary to prove her intellectual and social worth in the colonial world. However, her spunky behavior behind the teachers' backs shows that her feisty Antiguan spirit still thrives within.
Although Annie's father appears a gentle and reticent man, he serves as a testament to the unequal gender relations in Antigua. Annie's father is about thirty years older than his wife. He had numerous sexual affairs before marrying Annie's mother and the women with whom he slept frequently harass Annie's mother on the street. Now that he has his married life secured, he provides for the family while his wife takes care of his domestic and sexual needs. While as a man Annie's father could philander, Annie's mother interprets Annie's mere discussion with a group of boys as inappropriate sexual misconduct and calls her a "slut." With these two standards, it becomes clear that the behavior expected of men and women in Antigua are quite different. Although the women who curse at Annie's mother appear unfriendly, even Kincaid's depiction of them is sympathetic. They, after all, committed the same sexual act as Annie's father, but have been left in the difficult economic position of raising their children without a husband.