The relationships among the three main characters of Gardens in the Dunes reveal cultural conflicts between Native Americans and European Americans, as well as the larger social context of American heritage as understood in Europe in the nineteenth century.

Indigo is a Native American teenager of the Sand Lizard people, whose women maintain secret gardens in lands along the Arizona border with California. A raid by US military in which she is separated from her people leads to her education in an Indian boarding school. Indigo’s subsequent cultural whitening and her involvement with European American ethnobotanical scholarship shape her attitudes toward the gardens and toward cultural revitalization.

Hattie is a white woman who takes on Indigo’s tutelage and steers her toward assimilation. Her scholarship of ancient societies, both in the United States and England, is jeopardized by her marriage to Edward.

Hattie’s Aunt Bronwyn represents the innately feminine side of the earth and gardens; she aims to transmit to Hattie her reverence for European pagan traditions.

Edward Palmer, Hattie’s husband, is an older, scholarly white man. A botanist and archaeologist, he develops elaborate entrepreneurial schemes, ostensibly in support of scientific aims but ultimately destructive of the very plants he claims to appreciate. His professedly ignorant role in tropical collecting schemes, which build the famed Kew Gardens collections, stands for the Western colonialist, predominantly male exploitation that contrasts with an indigenous, fundamentally female appreciation of nature.