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Background and Purpose: Muscarinic acetylcholine receptors mediate alcohol consumption and seeking in rats. While M4 and M5 receptors have recently been implicated to mediate these behaviours in the striatum, their role in other brain regions remain unknown. The ventral tegmental area (VTA) and ventral subiculum (vSub) both densely express M4 and M5 receptors and modulate alcohol‐seeking, via their projections to the nucleus accumbens shell (AcbSh). Experimental Approach In Indiana alcohol‐preferring (iP) male rats, we examined Chrm4 (M4) and Chrm5 (M5) expression in the VTA and vSub following long‐term alcohol consumption and abstinence using RT‐qPCR. Using a combination of retrograde tracing and RNAscope, we examined the localisation of Chrm4 and Chrm5 on vSub cells that project to the AcbSh. Using selective allosteric modulators, we examined the functional role of M4 and M5 receptors within the vSub in alcohol consumption, context‐induced alcohol‐seeking, locomotor activity, and food/water consumption. Key Results: Long‐term alcohol and abstinence dysregulated the expression of genes for muscarinic receptors in the vSub, not in the VTA. Chrm4 was down‐regulated following long‐term alcohol and abstinence, while Chrm5 was up‐regulated following long‐term alcohol consumption. Consistent with these data, a positive allosteric modulator (VU0467154) of intra‐vSub M4 receptors reduced context‐induced alcohol‐seeking, but not motivation for alcohol self‐administration, while M5 receptor negative allosteric modulator (ML375) reduced initial motivation for alcohol self‐administration, but not context‐induced alcohol‐seeking. Conclusion and Implications: Collectively, our data highlight alcohol‐induced cholinergic dysregulation in the vSub and distinct roles for M4 and M5 receptor allosteric modulators to reduce alcohol consumption or seeking. [ABSTRACT FROM AUTHOR]