Prejudice is a central theme in Dance Hall of the Dead and other novels by Tony Hillerman. Set primarily on Navajo reservations, the novels address the relationship between Navajo and white society. The poverty, alcoholism, and crime common on the reservation are portrayed as in part a result of historic injustice and oppression and the Navajo religion and traditional culture are portrayed with great respect.

A second type of prejudice or tension that is shown is within Navajo culture between those who live on and those who live outside the reservation and between those who adhere to traditional ways and beliefs and those who have departed from them.

Another type of prejudice is shown in the relationship between the Navajo and Zunii tribes, whose uneasy relationships with each other actually predated the arrival of the Europeans in the southwest. The Navajo descended from nomadic tribes that moved south from Canada and invaded the lands originally farmed by the pueblo-dwelling ancestors of the Zuni and continued to raid the farms of the Zuni through the nineteenth century. The two tribes have different languages and traditions and the friendship between a Zuni and a Navajo is portrayed as somewhat unusual, as is the Navajo boy's desire to in a sense convert to Zuni tradition due to frustration with life in his own tribe.