The main theme of the story "Assimilation" is that people of different cultures or races often feel a sense of alienation when they decide to live in a white man's world. In addition to this, they also experience a continual sense of conflict over their choice to embrace this lifestyle instead of remaining true to the customs of their native origins.

This is why Mary Lynn's desire to cheat on her husband with an Indian man is so overwhelming. For example, Mary Lynn states that the attractiveness or status of the Indian man does not matter. She explains that the only thing required of her sexual partner is that he is an Indian. This fact reveals that deep inside Mary Lynn is driven by her need to reconnect to her Indian origins, perhaps because she believes she has betrayed her own people by leaving the reservation and assimilating into modern American society.

These feelings of betrayal as it relates to her native people are emphasized by the act of infidelity itself. Infidelity is a betrayal of one's marriage vows, and this acts as a symbol in the story. It represents Mary Lynn's desire to silence her feelings of betrayal to her people and assuage her guilt.

Perhaps this is also the reason that Mary Lynn experiences conflicted feelings for her husband Jeremiah. She tries to delude herself into believing that in her own marriage race is not an issue, but no matter how she tries, the effects of their racial differences still present themselves and cause division in their life together. This is symbolically shown in the contrasting looks of her children. Her sons look more Indian and receive different treatment than her daughter, who looks more white than her brothers.

At the end of the story, Mary Lynn's love for her husband is reaffirmed, but the reader is left with the feeling that the racial divide will continue to present itself in the couple's future.