Substance abuse disproportionately impacts American Indian/Alaska Native (AI/AN) communities in the United States. For the increasing numbers of AI/AN individuals who enter and receive treatment for their alcohol or other drug problem it is imperative that the service they receive be effective. This study used qualitative methodology to examine attitudes toward evidence-based practices, also known as evidence-based treatments (EBTs) in minority-serving substance abuse treatment programs in the San Francisco Bay area. Twenty-two interviews were conducted in the study, of which seven were with program directors and substance abuse counselors at two urban AI/AN focused sites. These clinics were more likely than other minority-focused programs to have experience with research and knowledge about adapting EBTs. Only in the AI/AN specific sites did an issue arise concerning visibility, that is, undercounting AI/AN people in national and state databases. Similar to other minority-focused programs, these clinics described mistrust, fear of exploitation from the research community, and negative attitudes towards EBTs. The underutilization of EBTs in substance abuse programs is prevalent and detrimental to the health of patients who would benefit from their use. Future research should explore how to use this research involvement and experience with adaptation to increase the adoption of EBTs in AI/AN serving clinics.