Background: Individuals with alcohol use disorder (AUD) can present with comorbid anxiety symptoms and often have deficits in emotional processing. Previous research suggests brain response is altered during facial affect recognition tasks, especially in limbic areas, due to either AUD or anxiety symptomology; however, the impact of both AUD and clinically significant anxiety symptoms during these tasks has not yet been examined. Methods: In this study, we investigated neural activation differences during an emotional facematching task. Participants (N = 232) underwent fMRI scanning, as part of a larger study. Three groups were investigated: individuals with diagnosed AUD and elevated anxiety traits (AUD + ANX, n = 90), individuals with diagnosed AUD but non-clinically significant levels of anxiety (AUD-ANX, n = 39), and healthy controls (HC, n = 103). Results: Our results illustrate distinct neurophenotypes of AUD, where individuals with comorbid anxiety symptomology have blunted emotional face processing while those with singular AUD are hyperresponsive. Conclusions: This suggests AUD with anxiety symptomology may have a unique neurobiological underpinning, and treatment and intervention should be tailored to individual constellations of symptoms.