Previous research with men who have sex with men (MSM) has found that substance use with sex is strongly associated with HIV acquisition and poor adherence to HIV treatments. Although some studies have assessed male couples' use of substances with unprotected anal sex, little is known on whether differences in their relationship dynamics are associated with their usage. Current HIV prevention initiatives underscore the importance of studying male couples' relationship dynamics. Using dyadic data from 28 HIV-positive and 58 HIV-discordant male couples, this analysis sought to: (1) describe, by substance type, whether neither, one, or both partners in the couple used a particular substance with sex within their relationship or outside of the relationship, respectively, and (2) assess, by substance type, whether relationship characteristic differences existed between these three groups of couples with respect to substance use with sex within and outside the relationship. Data from 86 dyads came from a cross-sectional, Internet study. Multivariate multinomial regression models were employed to achieve the aims. Except for alcohol, most did not use substances with sex. Within the relationship, those who used with sex varied by substance type; outside the relationship, most couples had only one partner who used with sex regardless of substance type. Several relationship characteristic differences were noted between the groups of couples. Within the relationship, marijuana and erectile dysfunction medication (EDM) use with sex was associated with having less tangible resources; for outside the relationship, these were associated with perceiving to have greater quality of alternatives. In general, amyl nitrates and party drug use with sex were associated with viewing the main partner as being less dependable for trustworthiness. Marijuana and party drug use with sex within the relationship and EDM use with sex outside the relationship were negatively associated with being able to communicate constructively. Mixed results were noted for relationship satisfaction. Additional research is urgently needed for prevention and promotion of healthy relationships for male couples who use substances with sex.