Alcohol misuse is associated with dysfunction of the amygdala-prefrontal cortical circuit. The amygdala and its cortical targets show decreased activity during a variety of task challenges in individuals engaged in problem drinking. On the other hand, it is less clear how amygdala resting state functional connectivity (rsFC) may be altered in association with alcohol misuse and whether such changes are restricted to prefrontal cortical structures. Further, the influences of comorbid substance use and depression and potential sex differences have not been assessed in earlier work. Here, with fMRI data from a Nathan Kline Institute/Rockland sample of 83 non-dependent alcohol drinkers (26 men), we addressed changes in whole brain rsFC of the amygdala in association with problem drinking as indexed by an alcohol involvement score. Imaging data were processed with Statistical Parametric Mapping following standard routines and all results were examined at voxel p < 0.001 uncorrected in combination with cluster p < 0.05 corrected for false discovery rate. Alcohol misuse was correlated with decreased amygdala connectivity with the dorsal anterior cingulate cortex (dACC) irrespective of depression and other substance use. Changes in amygdala-dACC connectivity manifested in the latero-basal subdivision of the amygdala. Further, men as compared to women showed a significantly stronger relationship in decreased amygdala-dACC connectivity and problem drinking, although it should be noted that men also showed a trend toward higher alcohol involvement score than women. The findings add to a growing literature documenting disrupted amygdala-prefrontal cortical functions in relation to alcohol misuse.