Squaraine dyes form aggregates in solution and in the solid state. We have found that squaraines form two-dimensional (2D) ordered layers when adsorbed onto HOPG from phenyloctane and from liquid crystalline solvents. We investigated with scanning tunneling microscopy the 2D structures of the adsorbed phases of five bis(4-alkylamino-2-hydroxyphenyl) squaraines (both symmetric and asymmetric) and mixtures of these squaraines. Differences in the stability of the 2D structures and molecular packing are observed when the alkyl tail length and symmetry are varied. A transition in the 2D structure from a herringbone packing to a lamellar packing occurs between the tail lengths of 4 carbons and 8 carbons. Many of the compounds form a number of 2D polytypes on HOPG. Multilayers of squaraine molecules were observed for most of the studied molecules. Squaraines with tail lengths of 12 carbons exhibited a tendency toward registry with the HOPG substrate whereas all other squaraine compounds investigated showed a lack of molecule- substrate registry. Domain sizes of the investigated molecules varied from tens of nanometers to a micron.