Ionic liquids (ILs) exhibit tunable behaviour and properties that are due to their supramolecular structure. We synthesized a series of alkylated and fluorinated phosphonium dicyanamide ILs to study the relation between molecular structure and assembly with a focus on the roles of cation chain length and fluorination. Small angle X-ray scattering indicated a lamellar structure with long-range order for all fluorinated ILs, while alkylated ILs showed only the general structures of ILs, i.e., alternating a polar ionic-zone and a nonpolar alkyl-zone. "Fluorophobic" interactions caused microphase segregation between perfluorinated and other molecular segments, "fluorophilic" interactions among the perfluorinated segments stabilized the microphase structure, and the coupling of "fluorophobic" and "fluorophilic" interactions resulted in a stable mesophase structure. The perfluorinated segments packed more densely than the alkylated analogues; the fluorinated versions (except for F2) liquefied at temperatures considerably above that of alkylated ILs. The lamellar structures strongly affected the rheology of the ILs. Fluorinated ILs had higher viscosities and exhibited non-Newtonian shear thinning; the alkylated ILs of the same length had an order of magnitude lower viscosities and were purely Newtonian. We propose that the disruption of lamellar structure in the shear flow causes the non-Newtonian flow behaviour.