We have reported here a comparative self-assembly and gelation studies of two isomeric bis-amide functionalized NDI-derivatives. In one case (NDI-1) the two amide groups were placed symmetrically on either side of the chromophore while for the other system (NDI-2) they were located on same side. In non-polar solvent both isomers formed self-assembled structures by synergistic effect of 𝜋-stacking and hydrogen-bonding. The propensity for self-assembly of NDI-1 was greater due to symmetrical placement of two amide groups on either arms of this chromophore which allowed 𝜋-stacking in tandem with hydrogen-bonding, while NDI-2 formed thermally more stable self-assembled fibres possibly due to location of two amide groups in close proximity along single arm of this chromophore. The structural difference in these two isomers lead to distinctly different morphology of their respective self-assembled structures which was further reflected on their gelation properties. Morphology of the self-assembled array of NDI-1 showed organized and regular entangled bundles of nanorods which imparted better gelation ability to this chromophore while the self-assembled fibres of NDI-2 showed less ordered and irregular fibres. We also probed self- assembly of these two chromophores in their mixture which revealed orthogonal assembly of the individual chromophores and no molecular mixing was noticed.