We have carried out a detailed atomic simulation study of molecular order within a chromonic liquid crystalline material (sunset yellow) in aqueous solution. Self-assembly occurs in dilute solutions to form stacked aggregates, which show a preference for head-to-tail stacking and antiparallel dipole order. This feature is independent of solution concentration and aggregate size. Stacks are found to be dynamic entities in which rotational transitions (flips) can occur between antiparallel and parallel configurations. At a concentration matching the nematic phase of sunset yellow, the simulations show chromonic columns with a loose hexagonal packing and an intercolumn distance of 2.36 nm. Partial condensation of sodium ions occurs around a chromonic stack, with two preferred binding sites identified for sodium ions, corresponding to strong binding with the oxygens of a sulfonate group and a bridging site between a pair of molecules in a stack. A value for the free energy of binding of a molecule to a stack of 7 kBT was obtained for stacks of three and eight molecules, with a slightly larger value (additional 2 kJ mo1-1) obtained for the dimer binding energy, indicating that aggregation is approximately isodesmic.