The effect of the anteiso-branch moiety of 18-MEA (18-methyleicosanic acid) to create a persistent hydrophobicity of alkaline-color-treated weathered hair treated with 18-MEA/SPDA (stearoxypropyldimethylamine) was investigated by comparing a straight-chain fatty acid (n-heneicosanoic acid, n-HEA) and an iso-branch fatty acid (19-methyleicosanic acid, 19-MEA) with the anteiso-branch fatty acid (18-MEA), using dynamic contact angle measurements, quantification of 18-MEA by LC/MS, and temperature controlled atomic force microscopy (AFM). The dynamic contact angle measurements indicated that the anteiso-branch moiety of 18-MEA is critical for the creation of a persistent hydrophobicity to alkaline-color-treated weathered hair. The temperature-controlled AFM investigations revealed that the anteiso-branch moiety of 18-MEA in the 18-MEA/SPDA system produces a persistent hydrophobicity to alkaline-color-treated weathered hair by providing higher fluidity to the upper region of the 18-MEA/SPDA layer.