Little research has examined differences in HIV stigma versus MSM stigma and the role of these stigmas in depression for HIV-positive Latino and African American men who have sex with men (MSM), subgroups disproportionately impacted by HIV in the US. MSM stigma, HIV stigma, depression, stress and social support were examined among HIV-positive Latino (n = 100) and African American (n = 99) MSM patients at five HIV clinics in Los Angeles County, California. In multiple regression models, Latino MSM had higher HIV stigma scores (p = 0.002) but lower MSM stigma scores (p < 0.001) compared to African American MSM. General support and stress were associated with HIV stigma (p < 0.001), but not MSM stigma. Both HIV stigma (p < 0.0001) and MSM stigma (p < 0.0001) were associated with depression. These data underscore the differences in experienced stigma for Latino and African American MSM and can be used to shape effective stigma reduction programs and behavioral counseling.