Children growing apart from their parents while becoming adolescents is the major theme in the novel. Annie and her mother share common personalities, goals and even look exactly alike, though they grow apart through the narrative. Barbara Wiedemann writes that Kincaid’s fiction is not specifically aimed at a young adult audience, but the readers will benefit from insight evident in Kincaid’s description of coming of age.
Annie John has been noted to contain feminist views. Asked if the relationship between Annie and Gwen was meant to suggest “lesbian tendencies,” Kincaid replied: "No…I think I am always surprised that people interpret it so literally." The relationship between Gwen and Annie is really a practicing relationship. It’s about how things work. It’s like learning to walk. Always there is the sense that they would go on to lead heterosexual lives. Whatever happened between then, homosexuality would not be a serious thing because it is just practicing” (Vorda 94).
In the story, the theme of colonization is conveyed. England has colonized Antigua, and has reconstructed its society. This is seen when the reader is introduced to Miss George and Miss Edward, teachers at Annie's school, who are both named after English kings. Antigua in return, strongly dislikes England for disposing of its native culture.
Water is consistently used throughout the novel to depict the separation between Annie John and her mother. Symbolic references to water (including the sea, rain, and other forms) illustrate Annie's development from childhood to maturity. Near the start of the novel, the reader learns that Annie has both a normal baby bottle and one shaped like a boat - and that is only the beginning of her water-connected choices in life.
Kincaid's writing form is not in the traditional paragraph form, but run-on sentences and paragraphs with little fragments. Jan Hall, a writer for Salem Press Master Plots, Fourth Edition book states in an article about Annie John that “because the novel has no years, months, or dates the story has a sense of timelessness.”