Molecular self-assembly provides a versatile tool for creating functional molecular structures at surfaces. A rational design of molecular structure formation requires not only an in-depth understanding of the subtle balance between intermolecular and molecule–surface interactions, but might also involve considering chemical changes of the molecules, such as deprotonation. Here, we present a systematic investigation of a comparatively simple class of molecules, namely dihydroxybenzoic acid, which, nevertheless, enables creating a rich variety of structures when deposited onto calcite (10.4) held at room temperature. Based on non-contact atomic force microscopy measurements in ultra-high vacuum, our study demonstrates the decisive impact of the positions of the hydroxyl groups on the structure formation. Six isomers of dihydroxybenzoic acid exist which form six different molecular structures on the calcite surface. Surprisingly, only two isomers arrange into stable, ordered structures at sub-monolayer coverage: 2,5-dihydroxybenzoic acid forms a commensurate (1 × 5) structure, composed of deprotonated molecules. A double-row structure consisting of protonated molecules is observed for 3,5-dihydroxybenzoic acid. The positions of the functional groups steer the molecular self-assembly of dihydroxybenzoic acids in three distinct ways, namely by (a) affecting the deprotonation tendency of the acid group, (b) influencing the intermolecular interaction as already indicated by greatly different bulk structures and (c) altering the molecule–substrate matching. Our results, thus, shed light on the impact of rather small changes in the molecular structure on the structural variety in molecular self-assembly on surfaces.