Self-organization in mono- and bilayers on HOPG of two groups of benz[5,6]acridino[2,1,9,8-klmna]acridine derivatives, namely, 8,16-dialkoxybenzo[h]benz[5,6]acridino[2,1,9,8-klmna]acridines with an increasing alkoxy substituent length and 8,16-bis(3- or 4- or 5-octylthiophen-2-yl)benzo[h]benz[5,6]acridino[2,1,9,8-klmna]acridines, i.e., three positional isomers of the same benzoacridine, is investigated by scanning tunneling microscopy. The layers were deposited from a solution of the adsorbate (in hexane or dichloromethane) and imaged ex situ at molecular resolution. In all cases, the resulting two-dimensional (2D) supramolecular organization is governed by the interactions between large, fused heteroaromatic cores that form densely packed rows separated by areas covered by substituents. In 8,16-dialkoxybenzo[h]benz[5,6]acridino[2,1,9,8-klmna]acridines, the alkoxy substituents, separating the rows of densely packed cores, are interdigitated. An increasing substituent length leads to an intuitively expected increase in this 2D unit cell parameter that corresponds to the orientation of the substituent in the monolayer. In the case of 8,16-bis(3- or 4- or 5-octylthiophen-2-yl)benzo[h]benz[5,6]acridino[2,1,9,8-klmna]acridine positional isomers, the self-assembly processes are more complex. Although the determined 2D unit cell is in all cases essentially the same, the role of alkylthienylene substituents in layer formation is distinctly different. Thus, the formation of monolayers and bilayers is very sensitive to isomerism. 8,16-Bis(5-octylthiophen-2-yl)benzo[h]benz[5,6]acridino[2,1,9,8-klmna]acridine is capable of forming the most stable monolayer and the most labile bilayer. In the case of 8,16-bis(3-octylthiophen-2-yl)benzo[h]benz[5,6]acridino[2,1,9,8-klmna]acridine, an inverse phenomenon is observed leading to the most labile monolayer and the most stable bilayer. These differences are rationalized in terms of dissimilar molecular geometries of the studied isomers and different interdigitation patterns in their 2D supramolecular structures.