This study examined gender differences in session one alliances and in the trajectory of the alliance over the course of couple therapy. Additionally, this study examined the association between men and women's pre‐therapy relationship adjustment and alliance at session one and over the course of therapy. A total of 316 couples seeking outpatient couple therapy were given the Locke–Wallace marital adjustment test at pre‐therapy to measure relationship adjustment and the session rating scale after each session to measure alliance with the therapist. The results showed that men had lower alliance ratings after session one than women. Men's pre‐therapy relationship adjustment was positively associated with their own session one alliance as well as their own alliance trajectory over the course of therapy. Men's pre‐therapy relationship adjustment was also positively associated with their partner's session one alliance. Women's pre‐therapy relationship adjustment showed no significant relationship with their own alliance or their partners at session one or the alliance trajectory over the course of therapy. The implications for how these gender differences may impact on the process of couple therapy with heterosexual couples are discussed. Practitioner points Initial alliances may differ for men and women in heterosexual couples and attending to reasons for seeking help may be instrumental. Partners’ pre‐therapy relationship distress can negatively impact on early alliance establishment; thus, more attention to the alliance may be needed for more distressed couples. Therapists may want to monitor the alliances in couple therapy to develop a better understanding of each partner's engagement in the process.