We have investigated the self-assembly behavior of fluorenyl-9-methoxycarbonyl (Fmoc)-FG, Fmoc-GG, and Fmoc-GF and compared it to that of Fmoc-FF using potentiometry, fluorescence and infrared spectroscopy, transmission electron microscopy, wide-angle X-ray scattering, and oscillatory rheometry. Titration experiments revealed a substantially shifted apparent pK(a) transition for Fmoc-FG, Fmoc-GG, and Fmoc-GF. The apparent pK(a) values observed correlated with the hydrophobicity (log P) of the Fmoc-dipeptide molecules. Fmoc-GG and Fmoc-GF were found to self-assemble only in their protonated form (below their apparent pK(a)), while Fmoc-FG formed self-assembled structures above and below its apparent pK(a). Fmoc-GG and Fmoc-FG were found to form hydrogels below their apparent pK(a) transitions in agreement with the entangled fibers morphologies revealed by TEM. Unlike Fmoc-FF and Fmoc-GG, Fmoc-FG showed unusual gelation behavior as gels were found to form upon heating. Fmoc-GF formed precipitates instead of a hydrogel below its apparent pK(a) in agreement with the formation of micrometer scale sheetlike structures observed by TEM. The fact that all four Fmoc-dipeptides were found to self-assemble suggests that the main driving force behind the self-assembly process is a combination of the hydrophobic and π-π interactions of the fluorenyl moieties with a secondary role for hydrogen bonding of the peptidic components. The nature of the peptidic tail was found to have a pronounced effect on the type of self-assembled structure formed. This work indicates that the substitution of phenylalanine by glycine significantly impacts on the mode of assembly and illustrates the versatility of aromatic peptide amphiphiles in the formation of structurally diverse nanostructures.