We have synthesized a series of amphiphiles wherein perylene diimide (hydrophobic unit) is appended with positively charged tyrosine-based alkyl amide (hydrophilic unit) at the -bay position (PDI 3a–3c). The optical and microscopic characterization of PDI 3a–3c and their Boc-protected derivatives PDI 2a–2c was carried out using UV-vis and fluorescence spectroscopy, atomic force microscopy, dynamic light scattering, polarimetric method, thermogravimetric analysis, electrochemical, density functional theory calculations and fluorescence microscopic techniques. The length of the alkyl chain on tyrosine alkyl amide revealed a great impact on the self-assembly and biolabeling properties of PDI 3a–3c. PDI 3a showed a fibrous network reminiscent of the ‘beehive’ nanostructure. The depth and diameter of the holes are 1.37 nm and 20–30 nm. PDI 3a and 3c have been successfully applied for biolabeling of human osteosarcoma MG-63 live cells. PDI 3b showed near IR (λ_em = 665 nm) ‘turn on’ fluorescence response for the nanomolar (0.98 nM) detection of sodium bis(2-ethylhexyl)sulfosuccinate (Na AOT) anionic surfactant based on (ionic)self-assembly in aqueous medium.